Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 99 of 126
Found at i:30130808 original size:59 final size:59
Alignment explanation
Indices: 30130695--30130868 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 59
30130685 GAAGATTCCT
* * * * *
30130695 AAACTTTCC-AAAAA-TCATATTTTGATCCCTAAACTTTCTAAAAATTCATATTTGATCCTA
1 AAACTTTCCAAAAAATTCA-AATTTAACCCCTAAACTTTCT-AAAATTTAGATTTGAT-CTA
* * * * *
30130755 AAACTTT-CTAAATATT-ACATTTTAACCCCTAATCTTTCTAAAATTTAGATTTGAATCTC
1 AAACTTTCCAAAAAATTCA-AATTTAACCCCTAAACTTTCTAAAATTTAGATTTG-ATCTA
* *
30130814 AAACTTTCCAAAAAATTCAAATTTAACCCTTAAACTTTCCAAAATTTAGATTTGA
1 AAACTTTCCAAAAAATTCAAATTTAACCCCTAAACTTTCTAAAATTTAGATTTGA
30130869 CCCTCGAAAG
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
59 23 0.24
60 70 0.74
61 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (59 bp):
AAACTTTCCAAAAAATTCAAATTTAACCCCTAAACTTTCTAAAATTTAGATTTGATCTA
Found at i:30130887 original size:60 final size:59
Alignment explanation
Indices: 30130775--30130890 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
30130765 AATATTACAT
* * * *
30130775 TTTAACCCCTAATCTTTCTAAAATTTAGATTTGAATCTCAAACTTTCCAAAAAATTCAAA
1 TTTAACCCCTAAACTTTCCAAAATTTAGATTTGAACCTCAAAC-GTCCAAAAAATTCAAA
* * *
30130835 TTTAACCCTTAAACTTTCCAAAATTTAGATTTGACCCTCGAAA-GTCCTAAAAATTC
1 TTTAACCCCTAAACTTTCCAAAATTTAGATTTGAACCTC-AAACGTCCAAAAAATTC
30130891 CATTTTGACC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 11 0.23
60 34 0.71
61 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (59 bp):
TTTAACCCCTAAACTTTCCAAAATTTAGATTTGAACCTCAAACGTCCAAAAAATTCAAA
Found at i:30131429 original size:104 final size:103
Alignment explanation
Indices: 30131246--30131451 Score: 277
Period size: 104 Copynumber: 2.0 Consensus size: 103
30131236 AAATATTTTC
* *
30131246 AAAATAGAGGCAATGTTTCTTTATTTAGGGAACTCGAGAAATTGTGCTCAAATGTATTGGGTACG
1 AAAATAGAGGCAATGTTTCTTTATTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGGGTACG
* * *
30131311 ATTTTTCTTCGAACCTAAGTAATTGAATATCTTATTCA
66 ATTGTTCTTCGAACCTAAATAATTGAATATCCTATTCA
* * * * * * * *
30131349 AAAATCGAGGTAATGTTTTTTTATTTTAGGGAAGTCGAGGAATTGTGCCCTAACGTGTTGGGTAT
1 AAAATAGAGGCAATGTTTCTTTA-TTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGGGTAC
*
30131414 GATTGTTCTTTGAACCTAAATAATTGAATATCCTATTC
65 GATTGTTCTTCGAACCTAAATAATTGAATATCCTATTC
30131452 GGAACCAATT
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
103 20 0.23
104 68 0.77
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (103 bp):
AAAATAGAGGCAATGTTTCTTTATTTAGGGAACTCGAGAAATTGTGCCCAAACGTATTGGGTACG
ATTGTTCTTCGAACCTAAATAATTGAATATCCTATTCA
Found at i:30137444 original size:3 final size:3
Alignment explanation
Indices: 30137436--30137468 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30137426 ATTGTCACAA
30137436 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30137469 CAAGGGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30138775 original size:12 final size:12
Alignment explanation
Indices: 30138757--30138786 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30138747 TTAATCTCAC
30138757 GAAGAAACAAAG
1 GAAGAAACAAAG
*
30138769 TAAGAAACAAAG
1 GAAGAAACAAAG
30138781 GAAGAA
1 GAAGAA
30138787 CTTTAGGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.23, T:0.03
Consensus pattern (12 bp):
GAAGAAACAAAG
Found at i:30139092 original size:55 final size:55
Alignment explanation
Indices: 30139033--30139142 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
30139023 AGCACACAAT
* *
30139033 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGTACAGCTGGCTGAG
1 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGACTGAG
* * *
30139088 CTATGCTCCCCTTTTTTTAGGTGGATCCTTCTAGTGCATTGCACAGCTGACTGAG
1 CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGACTGAG
30139143 ATGGCATGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.35
Consensus pattern (55 bp):
CTATGCTCCCCCTTTTTCAAGTGGATCCTTCTAGTGCATTGCACAGCTGACTGAG
Found at i:30141602 original size:6 final size:6
Alignment explanation
Indices: 30141591--30141617 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30141581 AAATCCCATT
30141591 AAAATC AAAATC AAAATC AAAATC AAA
1 AAAATC AAAATC AAAATC AAAATC AAA
30141618 TCCCTAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:30141897 original size:69 final size:68
Alignment explanation
Indices: 30141800--30141958 Score: 156
Period size: 69 Copynumber: 2.3 Consensus size: 68
30141790 ATAGGGAGCA
* * ** * *
30141800 GTTGCAGAGACGTGAAGAGGTAGGAATTGAATAGCAAAGCAGTTGCCAGAAAAAAAATAACAGCA
1 GTTGCAGAGAAGTGAAGAGGCAACAATTGAACAACAAAGCAGTTGCC-GAAAAAAAATAACAGCA
30141865 GAGG
65 GAGG
* ** * * *
30141869 GTTGTAGAGAAGTGAAGAGGCAACAATTGTCCAACAAAGCAGTTGTCGGAAAAAAATAATAGCAA
1 GTTGCAGAGAAGTGAAGAGGCAACAATTGAACAACAAAGCAGTTGCCGAAAAAAAATAACAGC-A
*
30141934 TAGGG
65 GA-GG
* *
30141939 GTTGCAAAGATGTGAAGAGG
1 GTTGCAGAGAAGTGAAGAGG
30141959 AAATTTTAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
68 14 0.19
69 39 0.54
70 19 0.26
ACGTcount: A:0.42, C:0.11, G:0.30, T:0.17
Consensus pattern (68 bp):
GTTGCAGAGAAGTGAAGAGGCAACAATTGAACAACAAAGCAGTTGCCGAAAAAAAATAACAGCAG
AGG
Found at i:30143821 original size:2 final size:2
Alignment explanation
Indices: 30143814--30143868 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
30143804 TAATCATAAC
*
30143814 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30143856 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
30143869 TACATTTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30146027 original size:24 final size:23
Alignment explanation
Indices: 30145996--30146068 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 23
30145986 ATAACACATT
30145996 AAAT-AATTATAATATTAAATAAA
1 AAATAAATTATAATATTAAAT-AA
*
30146019 AAATAAATTAAAATA-TAAATAA
1 AAATAAATTATAATATTAAATAA
* * *
30146041 AAAGAAATTTTAATAATTAAATTA
1 AAATAAATTATAAT-ATTAAATAA
30146065 AAAT
1 AAAT
30146069 TATTAAATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 13 0.32
23 10 0.24
24 18 0.44
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (23 bp):
AAATAAATTATAATATTAAATAA
Found at i:30150852 original size:70 final size:67
Alignment explanation
Indices: 30150733--30150865 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 67
30150723 ATAAACATTA
* ** *
30150733 TAATGGTTTTGCCTTTTAACTTAATGAATAAACATTTATTAAAACGACGTAGTTTTACCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACGACGTAGTTTTACCTTTTAA
30150798 TT
66 TT
30150800 TAATGGTTTTGACTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACGACGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTTAAC-TTAAAAAA--TAAACATTTATCAAAACGACGTAGTTTTACCTTT
30150865 T
63 T
30150866 CTTATTGGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 19 0.32
68 6 0.10
70 34 0.58
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAATAAACATTTATCAAAACGACGTAGTTTTACCTTTTAA
TT
Found at i:30153283 original size:11 final size:11
Alignment explanation
Indices: 30153267--30153291 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30153257 TCATGTTTTT
30153267 AAAAAAATTGA
1 AAAAAAATTGA
30153278 AAAAAAATTGA
1 AAAAAAATTGA
30153289 AAA
1 AAA
30153292 GTTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:30153325 original size:6 final size:5
Alignment explanation
Indices: 30153307--30153353 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 5
30153297 AAAAAATTAG
30153307 TTTA- TTTAT TTTCAT TTTCAT TTTAT TTTATT TTTATT TTTAT TTTA
1 TTTAT TTTAT TTT-AT TTT-AT TTTAT TTTA-T TTTA-T TTTAT TTTA
30153354 ATTATGCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.10
5 14 0.35
6 22 0.55
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:30153333 original size:17 final size:17
Alignment explanation
Indices: 30153311--30153353 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
30153301 AATTAGTTTA
30153311 TTTATTTTCATTTTCA-T
1 TTTATTTT-ATTTTCATT
*
30153328 TTTATTTTATTTTTATT
1 TTTATTTTATTTTCATT
30153345 TTTATTTTA
1 TTTATTTTA
30153354 ATTATGCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTTCATT
Found at i:30153339 original size:22 final size:21
Alignment explanation
Indices: 30153307--30153358 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
30153297 AAAAAATTAG
30153307 TTTATTTATTTTCATTTTCAT
1 TTTATTTATTTTCATTTTCAT
* *
30153328 TTTATTTTATTTTTATTTTTAT
1 TTTA-TTTATTTTCATTTTCAT
*
30153350 TTTAATTAT
1 TTTATTTAT
30153359 GCACTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTATTTTCATTTTCAT
Found at i:30154308 original size:12 final size:12
Alignment explanation
Indices: 30154293--30154334 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
30154283 AAAAAAAGAC
*
30154293 AAAAATAATCGA
1 AAAAATAATTGA
30154305 AAAAATAATTGA
1 AAAAATAATTGA
*
30154317 AAAAGAAAATTGA
1 AAAA-ATAATTGA
30154330 AAAAA
1 AAAAA
30154335 AAAAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAAATAATTGA
Found at i:30154320 original size:13 final size:13
Alignment explanation
Indices: 30154293--30154335 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
30154283 AAAAAAAGAC
*
30154293 AAAAATAATCG-A
1 AAAAATAATTGAA
30154305 AAAAATAATTGAA
1 AAAAATAATTGAA
30154318 AAAGAA-AATTGAA
1 AAA-AATAATTGAA
30154331 AAAAA
1 AAAAA
30154336 AAAGATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 12 0.43
13 14 0.50
14 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAATAATTGAA
Found at i:30155387 original size:25 final size:25
Alignment explanation
Indices: 30155367--30155412 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30155357 CCAATTAGAG
30155367 AATTAT-TATTTAG-ATTTAATTCA
1 AATTATCTATTTAGAATTTAATTCA
*
30155390 AATTATCTTTTTAGAATTTAATT
1 AATTATCTATTTAGAATTTAATT
30155413 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
AATTATCTATTTAGAATTTAATTCA
Found at i:30156812 original size:28 final size:27
Alignment explanation
Indices: 30156758--30156816 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
30156748 AAAACCTTCA
*
30156758 TGGCGATCTCTGCAAAGGACGCTTTTG
1 TGGCGATCTCTGCAAAGGACGCCTTTG
*
30156785 TGGCGAGTCTCTG-AAAGGAATGCCTTTG
1 TGGCGA-TCTCTGCAAAGG-ACGCCTTTG
30156813 TGGC
1 TGGC
30156817 TAGTACTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (27 bp):
TGGCGATCTCTGCAAAGGACGCCTTTG
Found at i:30158742 original size:38 final size:38
Alignment explanation
Indices: 30158649--30158823 Score: 217
Period size: 38 Copynumber: 4.6 Consensus size: 38
30158639 TATTGTTCAT
* * * * *
30158649 TTGAGCAAACA-TCAGTAAAATTAGTGGATTCGTTCAC
1 TTGAGCAAACATTCAGTATAATCAGTAGATTCGCTCGC
* * *
30158686 TTGGGCAAACATTTAGTATAATCAGTGGATTCGCTCGC
1 TTGAGCAAACATTCAGTATAATCAGTAGATTCGCTCGC
* * *
30158724 TTGAGCAAGCATTCAGTATAATCAATAGATTCACTCGC
1 TTGAGCAAACATTCAGTATAATCAGTAGATTCGCTCGC
* * *
30158762 TTGAGCAAGCATTCAATATAATTAGTAGATTCGCTCGC
1 TTGAGCAAACATTCAGTATAATCAGTAGATTCGCTCGC
30158800 TTGAGCAAACATTCAGTATAATCA
1 TTGAGCAAACATTCAGTATAATCA
30158824 ATATTCTTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
37 10 0.08
38 108 0.92
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (38 bp):
TTGAGCAAACATTCAGTATAATCAGTAGATTCGCTCGC
Found at i:30161465 original size:11 final size:11
Alignment explanation
Indices: 30161449--30161498 Score: 52
Period size: 10 Copynumber: 4.5 Consensus size: 11
30161439 CCCTTTTAAA
30161449 ATTTAAAAATT
1 ATTTAAAAATT
30161460 ATTTAAAAATT
1 ATTTAAAAATT
30161471 CA--TAAAAATT
1 -ATTTAAAAATT
30161481 A-TTAAAATATTT
1 ATTTAAAA-A-TT
30161493 ATTTAA
1 ATTTAA
30161499 GAAGTATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.03
10 13 0.38
11 12 0.35
12 4 0.12
13 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAAAAATT
Found at i:30162743 original size:11 final size:11
Alignment explanation
Indices: 30162727--30162761 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
30162717 ATCCCTTTGC
30162727 TCTTCATTATT
1 TCTTCATTATT
30162738 TCTTCATTATT
1 TCTTCATTATT
*
30162749 TGTTCATCTATT
1 TCTTCAT-TATT
30162761 T
1 T
30162762 ATAACCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.17, C:0.17, G:0.03, T:0.63
Consensus pattern (11 bp):
TCTTCATTATT
Found at i:30164683 original size:24 final size:25
Alignment explanation
Indices: 30164646--30164697 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
30164636 TAGGTTCTTT
*
30164646 TTCTTCTTTCTCTTCTTCCTT-TCC
1 TTCTTCTTTCTCTTCATCCTTCTCC
*
30164670 TTCTTC-TTCTTCTTGATCCTTCTCC
1 TTCTTCTTTC-TCTTCATCCTTCTCC
30164695 TTC
1 TTC
30164698 AACTGATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.62
25 6 0.25
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (25 bp):
TTCTTCTTTCTCTTCATCCTTCTCC
Found at i:30168296 original size:30 final size:30
Alignment explanation
Indices: 30168255--30168634 Score: 310
Period size: 30 Copynumber: 12.7 Consensus size: 30
30168245 GAGGCCCCCG
* * *
30168255 AACTTTGCAAAAATTATATTTTGACCCTTA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
* * * *
30168285 AACTTTTCAAAAATCACATTTTTA-CTTCTA
1 AACTTTTCCAAAATTACATTTTGACCCT-TA
* * *
30168315 AAC-TTTCCAAAATCATATTTTGACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
* *
30168344 AACTTTTTCAAAATTACATTTTGACACC-TG
1 AACTTTTCCAAAATTACATTTTGAC-CCTTA
* *
30168374 AACTTTTCCAAAATCACATTTTGACCCTTG
1 AACTTTTCCAAAATTACATTTTGACCCTTA
* *
30168404 AACTTTTCTAAAATTACATTTCGA-CCTTA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
** *
30168433 ATTTTTTCCAAAATTACATTTTAACCCTTA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
* * * *
30168463 AACTTCTCTAAAATTACATTTTAACCCCTCA
1 AACTTTTCCAAAATTACATTTTGA-CCCTTA
* * *
30168494 AAC-TTTCCAAAAAT-CATATTTAAACCTCTA
1 AACTTTTCCAAAATTACAT-TTTGACCCT-TA
*
30168524 AAC-TTTCCTAAAATCACATTTTGACCC-TA
1 AACTTTTCC-AAAATTACATTTTGACCCTTA
* *
30168553 AACTTTTCCAAAATTACATTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
** * * *
30168583 AACTTTTTTAAAATTACTTTTTTACCC-CA
1 AACTTTTCCAAAATTACATTTTGACCCTTA
**
30168612 AACTCATCCAAAATTACCATTTT
1 AACTTTTCCAAAATTA-CATTTT
30168635 ACTCCCGAAC
Statistics
Matches: 285, Mismatches: 51, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
29 89 0.31
30 173 0.61
31 20 0.07
32 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTGACCCTTA
Found at i:30168334 original size:59 final size:59
Alignment explanation
Indices: 30168272--30168635 Score: 333
Period size: 59 Copynumber: 6.1 Consensus size: 59
30168262 CAAAAATTAT
* * * * ** *
30168272 ATTTTGACCCTTAAACTTTTCAAAAATCACATTTTTACTTCTAAACTTTCCAAAATCAT
1 ATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTCCAAAATCAC
* * * *
30168331 ATTTTGACCCCTAAACTTTT-TCAAAATTACATTTTGACACCTGAACTTTTCCAAAATCAC
1 ATTTTAACCCTTAAACTTTTCT-AAAATTACATTTTGACCCCTAAAC-TTTCCAAAATCAC
* * * * ** *
30168391 ATTTTGACCCTTGAACTTTTCTAAAATTACATTTCGA-CCTTAATTTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCCTAA-ACTTTCCAAAATCAC
* * *
30168450 ATTTTAACCCTTAAACTTCTCTAAAATTACATTTTAACCCCTCAAACTTTCCAAAAATCAT
1 ATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCCT-AAACTTTCC-AAAATCAC
* * * *
30168511 A-TTTAAACCTCTAAACTTTCCTAAAATCACATTTTGA-CCCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCT-TAAACTTTTCTAAAATTACATTTTGACCCCTAAAC-TTTCCAAAATCAC
* * * * * *
30168570 ATTTTAACCCCTAAACTTTTTTAAAATTACTTTTTTACCCC-AAACTCATCCAAAATTACC
1 ATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCCTAAACT-TTCCAAAATCA-C
30168630 ATTTTA
1 ATTTTA
30168636 CTCCCGAACA
Statistics
Matches: 250, Mismatches: 42, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
58 1 0.00
59 131 0.52
60 86 0.34
61 32 0.13
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (59 bp):
ATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCCTAAACTTTCCAAAATCAC
Found at i:30168636 original size:29 final size:30
Alignment explanation
Indices: 30168439--30168662 Score: 96
Period size: 30 Copynumber: 7.5 Consensus size: 30
30168429 CTTAATTTTT
*
30168439 TCCAAAATTA-CATTTTAACCCTTAAACTTC-
1 TCCAAAATTACCATTTTAACCC-CAAAC-TCA
* *
30168469 TCTAAAATTA-CATTTTAACCCCTCAAACT-T
1 TCCAAAATTACCATTTTAA-CCC-CAAACTCA
* * *
30168499 TCCAAAA--ATCATATTTAAACCTCTAAACT-T
1 TCCAAAATTACCAT-TTT-AACC-CCAAACTCA
* * * **
30168529 TCCTAAAATCA-CATTTTGACCCTAAACTTT
1 TCC-AAAATTACCATTTTAACCCCAAACTCA
**
30168559 TCCAAAATTA-CATTTTAACCCCTAAACTTT
1 TCCAAAATTACCATTTTAACCCC-AAACTCA
** * *
30168589 TTTAAAATTA-CTTTTTTACCCCAAACTCA
1 TCCAAAATTACCATTTTAACCCCAAACTCA
*
30168618 TCCAAAATTACCATTTT-ACTCCCGAA--CA
1 TCCAAAATTACCATTTTAAC-CCCAAACTCA
30168646 TCCCAAAATTACCATTT
1 T-CCAAAATTACCATTT
30168663 GCACCTGAAC
Statistics
Matches: 162, Mismatches: 18, Indels: 29
0.78 0.09 0.14
Matches are distributed among these distances:
28 4 0.02
29 56 0.35
30 80 0.49
31 18 0.11
32 3 0.02
33 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACCATTTTAACCCCAAACTCA
Found at i:30168672 original size:28 final size:28
Alignment explanation
Indices: 30168619--30168690 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
30168609 CCAAACTCAT
*
30168619 CCAAAATTACCATTTTACTCCCGAACATC
1 CCAAAATTACCA-TTTACACCCGAACATC
* *
30168648 CCAAAATTACCATTTGCACCTGAACATC
1 CCAAAATTACCATTTACACCCGAACATC
**
30168676 TAAAAATTACCATTT
1 CCAAAATTACCATTT
30168691 TCTCCCCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCATTTACACCCGAACATC
Found at i:30176125 original size:39 final size:37
Alignment explanation
Indices: 30176060--30176428 Score: 160
Period size: 39 Copynumber: 9.5 Consensus size: 37
30176050 CCATCAACCA
*
30176060 ATCTCTTACCCCGAG-TCGAGGACAGATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCTTG-GG-CAGATT-CAGCCATCCG
* *
30176099 ATCTCTTACCCCGAGCTTAGGGCAGA-TCA-CTATCAGTCA
1 ATCTCTTACCCCGAGCTT-GGGCAGATTCAGCCATC---CG
* * ** *
30176138 ATCTCTTACCCCAAGCTTGGGGTAGATTGCAATCATTCG
1 ATCTCTTACCCCGAGCTT-GGGCAGATT-CAGCCATCCG
* *
30176177 ATCTTTTACCCCGAGCTTGAGGCAGA-TCA-CCATCAGCCA
1 ATCTCTTACCCCGAGCTTG-GGCAGATTCAGCCAT---CCG
* * *
30176216 ATCTCTTACCCCAAGCCTAGGGCAGATTGCAGTCATCCG
1 ATCTCTTACCCCGAG-CTTGGGCAGATT-CAGCCATCCG
* * * ** * *
30176255 ATCTCTTACCTCGAGCCTGGGCAGATCACAATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGCAGAT-TCAGCCATCCG
* * ** **
30176293 ATCTCTTACCCCGAACCTGAGGCAGATTACAGTAATTTG
1 ATCTCTTACCCCGAGCTTG-GGCAGATT-CAGCCATCCG
* * *
30176332 ATCTTTTACCCCGATCTTAGGGCAGA-TCA-CCATCAGCCA
1 ATCTCTTACCCCGAGCTT-GGGCAGATTCAGCCAT---CCG
* *
30176371 ATCTCTTTCCCCGAGGC-TGGGACAGATTACAGCCATTCG
1 ATCTCTTACCCCGA-GCTTGGG-CAGATT-CAGCCATCCG
* *
30176410 ATCTTTTACCACGAGCTTG
1 ATCTCTTACCCCGAGCTTG
30176429 AGGTAAATCA
Statistics
Matches: 247, Mismatches: 54, Indels: 58
0.69 0.15 0.16
Matches are distributed among these distances:
36 9 0.04
37 6 0.02
38 42 0.17
39 163 0.66
40 11 0.04
41 7 0.03
42 9 0.04
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (37 bp):
ATCTCTTACCCCGAGCTTGGGCAGATTCAGCCATCCG
Found at i:30176126 original size:78 final size:77
Alignment explanation
Indices: 30176021--30176486 Score: 445
Period size: 78 Copynumber: 6.0 Consensus size: 77
30176011 TGAAGATCTT
** * * * * *
30176021 ATCTTTTACCTTGAGCCTGGGGTAGATCACCATCAACCAATCTCTTACCCCGAGTCGAGGACAGA
1 ATCTTTTACCCCGAG-CTTGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCGAGGGCAGA
30176086 TTGCAGCCATCCG
65 TTGCAGCCATCCG
* * * * * *
30176099 ATCTCTTACCCCGAGCTTAGGGCAGATCACTATCAGTCAATCTCTTACCCCAAGCTTG-GGGTAG
1 ATCTTTTACCCCGAGCTT-GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC-CGAGGGCAG
** *
30176163 ATTGCAATCATTCG
64 ATTGCAGCCATCCG
* *
30176177 ATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCTTG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCGAGGGCAGA
*
30176242 TTGCAGTCATCCG
65 TTGCAGCCATCCG
* * * * *
30176255 ATCTCTTACCTCGAGCCTGGGCAGATCACAATCAGCCAATCTCTTACCCCGAACCTGA-GGCAGA
1 ATCTTTTACCCCGAGCTTGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCC-GAGGGCAGA
* ** **
30176319 TTACAGTAATTTG
65 TTGCAGCCATCCG
* * * *
30176332 ATCTTTTACCCCGATCTTAGGGCAGATCACCATCAGCCAATCTCTTTCCCCGAGGCTG-GGACAG
1 ATCTTTTACCCCGAGCTT-GGGCAGATCACCATCAGCCAATCTCTTACCCCGA-GCCGAGGGCAG
* *
30176396 ATTACAGCCATTCG
64 ATTGCAGCCATCCG
* * * * * *
30176410 ATCTTTTACCACGAGCTTGAGGTAAATCACTATCAGCTAATCTCTTACCCCGAG-CTAGGGGCAG
1 ATCTTTTACCCCGAGCTTG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCGA-GGGCAG
*
30176474 ATTGCAACCATCC
64 ATTGCAGCCATCC
30176487 AATATCTAAA
Statistics
Matches: 317, Mismatches: 60, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
77 67 0.21
78 248 0.78
79 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (77 bp):
ATCTTTTACCCCGAGCTTGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCGAGGGCAGAT
TGCAGCCATCCG
Found at i:30176454 original size:233 final size:234
Alignment explanation
Indices: 30176021--30176479 Score: 602
Period size: 233 Copynumber: 2.0 Consensus size: 234
30176011 TGAAGATCTT
* * * * **
30176021 ATCTTTTACCTTGAGCCTGGGGTAGATCACCATCAACCAATCTCTTACCCCGAGTCGAGGACAGA
1 ATCTCTTACCTCGAGCCTGGGGCAGATCACAATCAACCAATCTCTTACCCCGAACCGAGGACAGA
* * * *
30176086 TTGCAGCCATCCGATCTCTTACCCCGAGCTTAGGGCAGATCACTATCAGTCAATCTCTTACCCCA
66 TTACAGCAATCCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCCA
** * * * *
30176151 AGCTTGGGGTAGATTGCAATCATTCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
131 AGCTTGGGACAGATTACAACCATTCGATCTTTTACCACGAGCTTGAGGCAAATCACCATCAGCCA
30176216 ATCTCTTACCCCAAGCCTA-GGGCAGATTGCAGTCATCCG
196 ATCTCTTACCCCAAG-CTAGGGGCAGATTGCAGTCATCCG
*
30176255 ATCTCTTACCTCGAGCCT-GGGCAGATCACAATCAGCCAATCTCTTACCCCGAACCTGAGG-CAG
1 ATCTCTTACCTCGAGCCTGGGGCAGATCACAATCAACCAATCTCTTACCCCGAACC-GAGGACAG
* ** * * *
30176318 ATTACAGTAATTTGATCTTTTACCCCGATCTTAGGGCAGATCACCATCAGCCAATCTCTTTCCCC
65 ATTACAGCAATCCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCC
* * * *
30176383 GAGGC-TGGGACAGATTACAGCCATTCGATCTTTTACCACGAGCTTGAGGTAAATCACTATCAGC
130 -AAGCTTGGGACAGATTACAACCATTCGATCTTTTACCACGAGCTTGAGGCAAATCACCATCAGC
* *
30176447 TAATCTCTTACCCCGAGCTAGGGGCAGATTGCA
194 CAATCTCTTACCCCAAGCTAGGGGCAGATTGCA
30176480 ACCATCCAAT
Statistics
Matches: 193, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
232 3 0.02
233 167 0.87
234 23 0.12
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (234 bp):
ATCTCTTACCTCGAGCCTGGGGCAGATCACAATCAACCAATCTCTTACCCCGAACCGAGGACAGA
TTACAGCAATCCGATCTCTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCCA
AGCTTGGGACAGATTACAACCATTCGATCTTTTACCACGAGCTTGAGGCAAATCACCATCAGCCA
ATCTCTTACCCCAAGCTAGGGGCAGATTGCAGTCATCCG
Found at i:30178823 original size:30 final size:29
Alignment explanation
Indices: 30178789--30179012 Score: 142
Period size: 30 Copynumber: 7.5 Consensus size: 29
30178779 TAGAAATCAT
*
30178789 ATTTTGACCCTCAAATTTATCCAAAATTAC
1 ATTTTAACCCTCAAATTT-TCCAAAATTAC
* * *
30178819 ATTTTGACCCTCGAACTTTTCCTAAATTAC
1 ATTTTAACCCTC-AAATTTTCCAAAATTAC
* * *
30178849 ATTTAAACCC-C-AATCTCTTTCAGAATTAC
1 ATTTTAACCCTCAAAT-T-TTCCAAAATTAC
* *
30178878 ATTTTAACCC-CTAAACTTCTCTAAAATTAC
1 ATTTTAACCCTC-AAA-TTTTCCAAAATTAC
*
30178908 ATTTTAACCC-CTAAATTTTCCCAACA-T-C
1 ATTTTAACCCTC-AAATTTT-CCAAAATTAC
*
30178936 ATATTT-ACACCTCTAAACTTTCCTAAAATCT-C
1 AT-TTTAAC-CCTC-AAATTTTCC-AAAAT-TAC
30178968 ATTTTAA-CCTCACAATTTTCCAAAATTAC
1 ATTTTAACCCTCA-AATTTTCCAAAATTAC
*
30178997 ATTTTTAACCCCCAAA
1 A-TTTTAACCCTCAAA
30179013 CTCATCTAAA
Statistics
Matches: 156, Mismatches: 20, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 7 0.04
29 39 0.25
30 87 0.56
31 15 0.10
32 6 0.04
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTTTAACCCTCAAATTTTCCAAAATTAC
Found at i:30178886 original size:29 final size:30
Alignment explanation
Indices: 30178811--30179061 Score: 125
Period size: 30 Copynumber: 8.4 Consensus size: 30
30178801 AAATTTATCC
* * *
30178811 AAAATTACATTTTGA-CCCTCGAACTTTTCCT
1 AAAATTACATTTTAACCCCT-AAACTTCT-CT
* * *
30178842 -AAATTACATTTAAACCCC-AATC-TCTTT
1 AAAATTACATTTTAACCCCTAAACTTCTCT
*
30178869 CAGAATTACATTTTAACCCCTAAACTTCTCT
1 -AAAATTACATTTTAACCCCTAAACTTCTCT
* *
30178900 AAAATTACATTTTAACCCCTAAA-TTTTCCC
1 AAAATTACATTTTAACCCCTAAACTTCT-CT
* *
30178930 AACA-T-CATATTTACACCTCTAAACTT-TCCT
1 AAAATTACAT-TTTA-ACCCCTAAACTTCT-CT
* * *
30178960 AAAATCT-CATTTTAACCTC-ACAA-TTTTCC
1 AAAAT-TACATTTTAACCCCTA-AACTTCTCT
*
30178989 AAAATTACATTTTTAACCCCCAAAC-TCATCT
1 AAAATTACA-TTTTAACCCCTAAACTTC-TCT
* * *
30179020 AAAATTACCATTTT-ACCCCCAAACATC-CA
1 AAAATTA-CATTTTAACCCCTAAACTTCTCT
30179049 AAAATTACCATTT
1 AAAATTA-CATTT
30179062 CCCTCGAACA
Statistics
Matches: 178, Mismatches: 22, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 6 0.03
29 51 0.29
30 85 0.48
31 29 0.16
32 6 0.03
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTCTCT
Found at i:30179014 original size:60 final size:58
Alignment explanation
Indices: 30178797--30179034 Score: 184
Period size: 60 Copynumber: 4.0 Consensus size: 58
30178787 ATATTTTGAC
* * * *
30178797 CCTCAAATTTATCCAAAATTACATTTTGACCCTCGAACTTTTCCT-AAATTACATTTAAA
1 CCTCAAATTT-TCCAAAATTACATTTTAACCCCCAAAC-TTTCCTAAAATTACATTTTAA
* * * *
30178856 CC-CCAATCTCTTTCAGAATTACATTTTAACCCCTAAAC-TTCTCTAAAATTACATTTTAA
1 CCTCAAAT-T-TTCCAAAATTACATTTTAACCCCCAAACTTTC-CTAAAATTACATTTTAA
* * * *
30178915 CCCCTAAATTTTCCCAACA-T-CATATTTACACCTCTAAACTTTCCTAAAATCT-CATTTTAA
1 CCTC-AAATTTT-CCAAAATTACAT-TTTA-ACCCCCAAACTTTCCTAAAAT-TACATTTTAA
*
30178975 CCTCACAATTTTCCAAAATTACATTTTTAACCCCCAAACTCAT-CTAAAATTACCATTTTA
1 CCTCA-AATTTTCCAAAATTACA-TTTTAACCCCCAAACT-TTCCTAAAATTA-CATTTTA
30179035 CCCCCAAACA
Statistics
Matches: 143, Mismatches: 18, Indels: 34
0.73 0.09 0.17
Matches are distributed among these distances:
57 3 0.02
58 9 0.06
59 53 0.37
60 56 0.39
61 21 0.15
62 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (58 bp):
CCTCAAATTTTCCAAAATTACATTTTAACCCCCAAACTTTCCTAAAATTACATTTTAA
Found at i:30197534 original size:16 final size:17
Alignment explanation
Indices: 30197503--30197535 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30197493 TAATTTTTTA
30197503 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
30197521 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
30197536 CTGTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:30197571 original size:17 final size:16
Alignment explanation
Indices: 30197551--30197596 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30197541 ATTATATATA
30197551 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
30197568 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
30197584 CT-ATAAA-ATTAAA
1 -TAATAAATATTAAA
30197597 CTTTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:30197583 original size:16 final size:17
Alignment explanation
Indices: 30197551--30197583 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30197541 ATTATATATA
30197551 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
30197568 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
30197584 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:30197638 original size:24 final size:25
Alignment explanation
Indices: 30197611--30197664 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
30197601 AATGATAATA
30197611 TAATAATATAATATAT-ACTACTAC
1 TAATAATATAATATATAACTACTAC
* *
30197635 TAATAATATAATATGTAACTATTAC
1 TAATAATATAATATATAACTACTAC
30197660 TAATA
1 TAATA
30197665 CATGATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (25 bp):
TAATAATATAATATATAACTACTAC
Found at i:30200515 original size:24 final size:24
Alignment explanation
Indices: 30200488--30200533 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
30200478 TAATATTTTA
*
30200488 ATATATGAAAT-ATTAATTTTAAAT
1 ATATAT-AAATAATTAATATTAAAT
*
30200512 ATATCTAAATAATTAATATTAA
1 ATATATAAATAATTAATATTAA
30200534 TTATTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATAAATAATTAATATTAAAT
Found at i:30203107 original size:30 final size:30
Alignment explanation
Indices: 30203073--30203146 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
30203063 AAGTTTGAAA
30203073 TGATTGAGAAAGCAAGAGAGAATGTTGCTT
1 TGATTGAGAAAGCAAGAGAGAATGTTGCTT
30203103 TGATTGAGAAAGCAAGAGAGAATGTTGCTT
1 TGATTGAGAAAGCAAGAGAGAATGTTGCTT
30203133 TGATTGAGAAAGCA
1 TGATTGAGAAAGCA
30203147 GTTTGGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.38, C:0.07, G:0.30, T:0.26
Consensus pattern (30 bp):
TGATTGAGAAAGCAAGAGAGAATGTTGCTT
Found at i:30203979 original size:25 final size:22
Alignment explanation
Indices: 30203926--30203976 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
30203916 AAAGAATCAT
*
30203926 GTCACGATGATGTTCATTCGAG
1 GTCACGATGATGCTCATTCGAG
30203948 GTCACGATGATGCTCATTCGAG
1 GTCACGATGATGCTCATTCGAG
30203970 GTCACGA
1 GTCACGA
30203977 CGAGAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
GTCACGATGATGCTCATTCGAG
Found at i:30207596 original size:34 final size:35
Alignment explanation
Indices: 30207557--30207632 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
30207547 AATAAAATAT
* *
30207557 TATTTTTATTAAATTAAATTTTGA-ATTGGATTTTA
1 TATTTTTA-CAAATTAAATTTGGATATTGGATTTTA
**
30207592 -ATTTTTACAAATTGTATTTGGATATTGGATTTTA
1 TATTTTTACAAATTAAATTTGGATATTGGATTTTA
30207626 TATTTTT
1 TATTTTT
30207633 TTATTTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 11 0.31
34 18 0.51
35 6 0.17
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (35 bp):
TATTTTTACAAATTAAATTTGGATATTGGATTTTA
Found at i:30214062 original size:19 final size:20
Alignment explanation
Indices: 30214027--30214067 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30214017 TATTAGCATG
*
30214027 ATAAAAAAATTCTAAAT-AA
1 ATAAAAAAATTCAAAATGAA
30214046 ATAACAAAAATT-AAAATGAA
1 ATAA-AAAAATTCAAAATGAA
30214066 AT
1 AT
30214068 CATCATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
ATAAAAAAATTCAAAATGAA
Found at i:30219159 original size:16 final size:16
Alignment explanation
Indices: 30219138--30219173 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30219128 ACTAACTAAT
*
30219138 AACTGCTTACTGCAGA
1 AACTGCTAACTGCAGA
*
30219154 AACTGCTAACTGCAGT
1 AACTGCTAACTGCAGA
30219170 AACT
1 AACT
30219174 AACTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (16 bp):
AACTGCTAACTGCAGA
Found at i:30220871 original size:24 final size:24
Alignment explanation
Indices: 30220826--30220872 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30220816 ATTTAGTAGT
*
30220826 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
30220850 ATAATATATTTTA-CATTGATTAG
1 ATAATATA-TTTAGCATTGATTAG
30220873 ATTTAGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:30224467 original size:24 final size:26
Alignment explanation
Indices: 30224413--30224462 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
30224403 TTTTTCCAGA
* *
30224413 ACATTTAGTAGTATAATATATTTTTG
1 ACATTTATTAGCATAATATATTTTTG
*
30224439 GCATTTATTAGCATAATATATTTT
1 ACATTTATTAGCATAATATATTTT
30224463 ACATTGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (26 bp):
ACATTTATTAGCATAATATATTTTTG
Found at i:30224472 original size:24 final size:26
Alignment explanation
Indices: 30224425--30224473 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
30224415 ATTTAGTAGT
* *
30224425 ATAATATATTTTTGGCATTTATTAGC
1 ATAATATATTTTTGACATTGATTAGC
30224451 ATAATATA-TTTT-ACATTGATTAG
1 ATAATATATTTTTGACATTGATTAG
30224474 AATTAGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (26 bp):
ATAATATATTTTTGACATTGATTAGC
Found at i:30227757 original size:13 final size:13
Alignment explanation
Indices: 30227741--30227765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30227731 CTATATATAA
30227741 TTACTACTAAATG
1 TTACTACTAAATG
30227754 TTACTACTAAAT
1 TTACTACTAAAT
30227766 AAACAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TTACTACTAAATG
Found at i:30230630 original size:2 final size:2
Alignment explanation
Indices: 30230625--30230674 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
30230615 TGAGAAACCA
30230625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30230667 AT AT AT AT
1 AT AT AT AT
30230675 TATTTTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30232042 original size:14 final size:14
Alignment explanation
Indices: 30232025--30232075 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
30232015 TCATAAATGC
*
30232025 GGATTCATAGGGGT
1 GGATTCATAGAGGT
*
30232039 GGATTCATAAAGGT
1 GGATTCATAGAGGT
*
30232053 GGACTT-ATAGATGT
1 GGA-TTCATAGAGGT
30232067 GGATTCATA
1 GGATTCATA
30232076 CATGCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 2 0.06
14 27 0.87
15 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.31
Consensus pattern (14 bp):
GGATTCATAGAGGT
Found at i:30232062 original size:28 final size:28
Alignment explanation
Indices: 30232012--30232075 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
30232002 TTTACATGTA
* *
30232012 GATTCATAAATGCGGATTCATAGGGGTG
1 GATTCATAAAGGCGGATTCATAGAGGTG
* *
30232040 GATTCATAAAGGTGGACTT-ATAGATGTG
1 GATTCATAAAGGCGGA-TTCATAGAGGTG
30232068 GATTCATA
1 GATTCATA
30232076 CATGCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (28 bp):
GATTCATAAAGGCGGATTCATAGAGGTG
Found at i:30232832 original size:19 final size:18
Alignment explanation
Indices: 30232810--30232862 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
30232800 TCCTATTATA
30232810 ATTTTTCCTTCCTTTCTTT
1 ATTTTTCCTT-CTTTCTTT
30232829 ATTTCTTCCTTCTTTCTTT
1 ATTT-TTCCTTCTTTCTTT
30232848 -TCTTTTCCTTTCTTT
1 AT-TTTTCC-TTCTTT
30232863 ACATCATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.16
19 20 0.65
20 6 0.19
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTCCTTCTTTCTTT
Found at i:30232838 original size:16 final size:16
Alignment explanation
Indices: 30232817--30232863 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
30232807 ATAATTTTTC
30232817 CTTCCTTTCTTTATTT
1 CTTCCTTTCTTTATTT
*
30232833 CTTCC-TTCTTTCTTTT
1 CTTCCTTTCTTT-ATTT
30232849 CTTTTCCTTTCTTTA
1 C--TTCCTTTCTTTA
30232864 CATCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 6 0.24
16 9 0.36
18 4 0.16
19 6 0.24
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTCCTTTCTTTATTT
Found at i:30233851 original size:21 final size:22
Alignment explanation
Indices: 30233801--30233851 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
30233791 AATAATTCAT
*
30233801 GAAAT-AATGTAGACTTCTACC
1 GAAATAAATGAAGACTTCTACC
***
30233822 GATGCAAATGAAG-CTTCTACC
1 GAAATAAATGAAGACTTCTACC
30233843 GAAATAAAT
1 GAAATAAAT
30233852 CATGCTTTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (22 bp):
GAAATAAATGAAGACTTCTACC
Found at i:30234525 original size:3 final size:3
Alignment explanation
Indices: 30234517--30234558 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
30234507 AAAATTCCAA
*
30234517 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
30234559 CCAAAATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30234946 original size:2 final size:2
Alignment explanation
Indices: 30234939--30234966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30234929 CATGATTATC
30234939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30234967 TAAGTAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30235663 original size:7 final size:7
Alignment explanation
Indices: 30235648--30235697 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
30235638 AAAAAAAAGT
*
30235648 AACGGTC
1 AACGATC
30235655 AACGATC
1 AACGATC
*
30235662 AACGGTC
1 AACGATC
30235669 AACGATC
1 AACGATC
*
30235676 AAAG-TC
1 AACGATC
*
30235682 AACGGTC
1 AACGATC
30235689 AACGATC
1 AACGATC
30235696 AA
1 AA
30235698 AGTCATCGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (7 bp):
AACGATC
Found at i:30235667 original size:14 final size:14
Alignment explanation
Indices: 30235648--30235697 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
30235638 AAAAAAAAGT
30235648 AACGGTCAACGATC
1 AACGGTCAACGATC
30235662 AACGGTCAACGATC
1 AACGGTCAACGATC
* *
30235676 AA-AGTCAACGGTC
1 AACGGTCAACGATC
*
30235689 AACGATCAA
1 AACGGTCAA
30235698 AGTCATCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (14 bp):
AACGGTCAACGATC
Found at i:30235685 original size:20 final size:20
Alignment explanation
Indices: 30235660--30235708 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
30235650 CGGTCAACGA
30235660 TCAACGGTCAACGATCAAAG
1 TCAACGGTCAACGATCAAAG
30235680 TCAACGGTCAACGATCAAAG
1 TCAACGGTCAACGATCAAAG
*
30235700 TCATCGGTC
1 TCAACGGTC
30235709 GGTCAACGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
TCAACGGTCAACGATCAAAG
Found at i:30236232 original size:17 final size:16
Alignment explanation
Indices: 30236206--30236263 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
30236196 AAGAAAATAA
30236206 AAAAGAAAAGAGAAAGG
1 AAAAG-AAAGAGAAAGG
*
30236223 AATAAGAAAG-GAATGAGA
1 AA-AAGAAAGAGAA--AGG
30236241 AAAAGAAAAGAGAAAGG
1 AAAAG-AAAGAGAAAGG
30236258 AAAAGA
1 AAAAGA
30236264 TGAGAGGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 4 0.12
17 16 0.47
18 11 0.32
19 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAGAAAGG
Found at i:30236232 original size:22 final size:22
Alignment explanation
Indices: 30236201--30236242 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
30236191 AGAGGAAGAA
30236201 AATAAAAAAGAAAAGAGAAAGG
1 AATAAAAAAGAAAAGAGAAAGG
* * *
30236223 AATAAGAAAGGAATGAGAAA
1 AATAAAAAAGAAAAGAGAAA
30236243 AAGAAAAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (22 bp):
AATAAAAAAGAAAAGAGAAAGG
Found at i:30241659 original size:3 final size:3
Alignment explanation
Indices: 30241651--30241698 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
30241641 AACATTCCAA
*
30241651 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
30241697 AA
1 AA
30241699 CCAAAATGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30242794 original size:20 final size:20
Alignment explanation
Indices: 30242769--30242828 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
30242759 TTCGAAAAAA
*
30242769 GTCAACGATCAAAATCAACG
1 GTCAACGATCAAAGTCAACG
* *
30242789 GTCAACGATCAACGGTCAA-A
1 GTCAACGATCAA-AGTCAACG
30242809 GTCAACGATCAAAGTCAACG
1 GTCAACGATCAAAGTCAACG
30242829 ATCGGTCAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 5 0.15
20 24 0.73
21 4 0.12
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
GTCAACGATCAAAGTCAACG
Found at i:30242799 original size:14 final size:14
Alignment explanation
Indices: 30242766--30242828 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 14
30242756 TTTTTCGAAA
*
30242766 AAAG-TCAACGATC
1 AAAGATCAACGGTC
30242779 AAA-ATCAACGGTC
1 AAAGATCAACGGTC
*
30242792 AACGATCAACGGTC
1 AAAGATCAACGGTC
*
30242806 AAAG-TCAACGATC
1 AAAGATCAACGGTC
30242819 AAAG-TCAACG
1 AAAGATCAACG
30242829 ATCGGTCAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
13 31 0.70
14 13 0.30
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAGATCAACGGTC
Found at i:30243334 original size:12 final size:12
Alignment explanation
Indices: 30243317--30243364 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
30243307 TTATAAGAGG
*
30243317 AAGAAAATAGAA
1 AAGAAAAGAGAA
30243329 AAGAAAAGAG-A
1 AAGAAAAGAGAA
* *
30243340 AAGGAATGAGAAA
1 AAGAAAAGAG-AA
30243353 AAGAAAAGAGAA
1 AAGAAAAGAGAA
30243365 CGGAAAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
11 9 0.31
12 11 0.38
13 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (12 bp):
AAGAAAAGAGAA
Found at i:30243337 original size:23 final size:24
Alignment explanation
Indices: 30243311--30243364 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
30243301 GTGTGATTAT
*
30243311 AAGAGGAAGAAAAT-AG-AAAAGAA
1 AAGAGAAAG-AAATGAGAAAAAGAA
*
30243334 AAGAGAAAGGAATGAGAAAAAGAA
1 AAGAGAAAGAAATGAGAAAAAGAA
30243358 AAGAGAA
1 AAGAGAA
30243365 CGGAAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 10 0.37
24 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.04
Consensus pattern (24 bp):
AAGAGAAAGAAATGAGAAAAAGAA
Found at i:30243866 original size:28 final size:28
Alignment explanation
Indices: 30243822--30243875 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
30243812 GATATCCGAT
*
30243822 TTACTCCCTATTGACCCAAAGGTCATAC
1 TTACTCCCTATTAACCCAAAGGTCATAC
30243850 TTACTCCCTATTAACCCAAAGGTCAT
1 TTACTCCCTATTAACCCAAAGGTCAT
30243876 GATGCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (28 bp):
TTACTCCCTATTAACCCAAAGGTCATAC
Found at i:30243903 original size:36 final size:36
Alignment explanation
Indices: 30243850--30243948 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
30243840 AAGGTCATAC
* *
30243850 TTACTCCCTATTAACCCAAAGGTCATGATGCTT-ATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATG-TTCATT
30243886 TTACTCCCTGTTGACCCAAAGGTCATGATGTTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGTTCATT
*
30243922 TTACTCCCTGTTGACCTAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
30243949 CCTATTACCA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 2 0.03
36 57 0.97
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGGTCATGATGTTCATT
Found at i:30247664 original size:5 final size:5
Alignment explanation
Indices: 30247623--30247662 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
30247613 ACTCTGATTT
*
30247623 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC TTCTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC
30247663 TTTCTATTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (5 bp):
CTCTC
Found at i:30256012 original size:21 final size:20
Alignment explanation
Indices: 30255988--30256029 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30255978 AAAGTATACT
*
30255988 TTTTTTTAGTTTCGCCTTTAA
1 TTTTTTTAGTTTC-ACTTTAA
*
30256009 TTTTTTTTGTTTCACTTTAA
1 TTTTTTTAGTTTCACTTTAA
30256029 T
1 T
30256030 CCTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTTTTAGTTTCACTTTAA
Found at i:30256026 original size:20 final size:22
Alignment explanation
Indices: 30255987--30256029 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
30255977 TAAAGTATAC
*
30255987 TTTTTTTTAGTTTCGCCTTTAA
1 TTTTTTTTAGTTTCGACTTTAA
30256009 TTTTTTTT-GTTTC-ACTTTAA
1 TTTTTTTTAGTTTCGACTTTAA
30256029 T
1 T
30256030 CCTTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTTTTTTAGTTTCGACTTTAA
Found at i:30256219 original size:33 final size:32
Alignment explanation
Indices: 30256173--30256236 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
30256163 TTAGAAATGA
*
30256173 AAAAAATAGAAAAAAATTACAAAAATAATTAT
1 AAAAAATAAAAAAAAATTACAAAAATAATTAT
* *
30256205 AAAAAATAAAAAAAAGCTTACAAAAATTATTA
1 AAAAAATAAAAAAAA-ATTACAAAAATAATTA
30256237 AAATTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (32 bp):
AAAAAATAAAAAAAAATTACAAAAATAATTAT
Found at i:30256479 original size:27 final size:27
Alignment explanation
Indices: 30256445--30256499 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
30256435 TAGAACTTAT
*
30256445 AATTAGTAGATTTTTTTAAGTA-ATAA
1 AATTAGTAGATTTTTTAAAGTATATAA
*
30256471 AATTGAGTATATTTTTTAAAGTATATAA
1 AATT-AGTAGATTTTTTAAAGTATATAA
30256499 A
1 A
30256500 TAATGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 16 0.64
28 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (27 bp):
AATTAGTAGATTTTTTAAAGTATATAA
Found at i:30257482 original size:3 final size:3
Alignment explanation
Indices: 30257476--30257507 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30257466 CATCATCATT
30257476 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
30257508 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:30257512 original size:3 final size:3
Alignment explanation
Indices: 30257506--30257552 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
30257496 ATAATAATAA
30257506 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30257553 ATTTGAGTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:30258054 original size:113 final size:113
Alignment explanation
Indices: 30257911--30258135 Score: 342
Period size: 113 Copynumber: 2.0 Consensus size: 113
30257901 AATCGTATTG
* * * *
30257911 TTGTATGGACAAATTAGAGGTCAGTGGTCACATGCTAAATACTAAACAAGTACTATTATTGCAAG
1 TTGTATGAACAAATTAGAGGTCAATGGTCACATGCTAAATACCAAACAAGTACTACTATTGCAAG
* * *
30257976 TTGGTTATTATTATGATACGTGTTGCATGGTTTCACTTGTGTCATAAA
66 TTGGTTATTATTATGATACGTGTTACATAGTTCCACTTGTGTCATAAA
* * * *
30258024 TTGTATGAACAAGTTAGAGGTCAATGGTCACATGCTAAATGCCAAACGAGTATTACTATTGCAAG
1 TTGTATGAACAAATTAGAGGTCAATGGTCACATGCTAAATACCAAACAAGTACTACTATTGCAAG
*
30258089 TTGGTTATTATTATGATACGTGTTACGTAGTTCCACTTGTGTCATAA
66 TTGGTTATTATTATGATACGTGTTACATAGTTCCACTTGTGTCATAA
30258136 GTTATCTTGT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 100 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (113 bp):
TTGTATGAACAAATTAGAGGTCAATGGTCACATGCTAAATACCAAACAAGTACTACTATTGCAAG
TTGGTTATTATTATGATACGTGTTACATAGTTCCACTTGTGTCATAAA
Found at i:30261025 original size:28 final size:28
Alignment explanation
Indices: 30260994--30261058 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
30260984 TCGAAGAATC
*
30260994 ACCACAGAGACATCCTTAAACAAAGATA
1 ACCACAAAGACATCCTTAAACAAAGATA
* *
30261022 ACCACAAAGGCGTCCTTAAACAAAGATA
1 ACCACAAAGACATCCTTAAACAAAGATA
*
30261050 ACTACAAAG
1 ACCACAAAG
30261059 GCTTTCCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.49, C:0.25, G:0.12, T:0.14
Consensus pattern (28 bp):
ACCACAAAGACATCCTTAAACAAAGATA
Found at i:30261059 original size:28 final size:28
Alignment explanation
Indices: 30261006--30261060 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
30260996 CACAGAGACA
30261006 TCCTTAAACAAAGATAACCACAAAGGCG
1 TCCTTAAACAAAGATAACCACAAAGGCG
*
30261034 TCCTTAAACAAAGATAACTACAAAGGC
1 TCCTTAAACAAAGATAACCACAAAGGC
30261061 TTTCCCATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (28 bp):
TCCTTAAACAAAGATAACCACAAAGGCG
Found at i:30261215 original size:28 final size:28
Alignment explanation
Indices: 30261128--30261220 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 28
30261118 TTTTACATCT
*
30261128 GCCACGAAGGCTTCCTTTAATAGAGTTA
1 GCCACGAAGGCTTCCTTTAACAGAGTTA
* *
30261156 GACACGAAAGCTTCCTTTAACAGAGTTA
1 GCCACGAAGGCTTCCTTTAACAGAGTTA
* *
30261184 GCCACGAAGGCTTCCTTTAACAGAATTC
1 GCCACGAAGGCTTCCTTTAACAGAGTTA
30261212 GCCAC-AAGG
1 GCCACGAAGG
30261221 GTTTTCCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
27 4 0.07
28 54 0.93
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (28 bp):
GCCACGAAGGCTTCCTTTAACAGAGTTA
Found at i:30267473 original size:15 final size:17
Alignment explanation
Indices: 30267445--30267476 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
30267435 ACAATTTAAA
30267445 ATTTTTATATAAAAAAT
1 ATTTTTATATAAAAAAT
30267462 ATTTTT-TA-AAAAAAT
1 ATTTTTATATAAAAAAT
30267477 CATATGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTATATAAAAAAT
Found at i:30273710 original size:287 final size:288
Alignment explanation
Indices: 30273189--30273767 Score: 1070
Period size: 287 Copynumber: 2.0 Consensus size: 288
30273179 TCTTTTGCTT
30273189 CTCTATGTGGCACAAGCATTTCTAGTTGTCGTCTTTCCAAGTTTCTTCATTCTAGATTCTGTTCC
1 CTCTATGTGGCACAAGCATTTCTAGTTGTCGTCTTTCCAAGTTTCTTCATTCTAGATTCTGTTCC
*
30273254 CTTTCTATGGCAACAATAGTATTGGTCTGATGGCCCATTTTCTTTCTTCTAATGATTGATTTTAT
66 CTTTCTATGGCAACAATAGTATTGGTCCGATGGCCCATTTTCTTTCTTCTAATGATTGATTTTAT
* *
30273319 ACTCTTCCCTCCATTTGTGAGCATGCGTTTAATTGGGTGATATTTGTAAACGAGTTTTTGTGCCA
131 ACTCTTCCCTCCATTTGTGAGCATGCGTGTAATTGGGTGATATTTATAAACGAGTTTTTGTGCCA
*
30273384 CATTTCACTAGAACTGTTCTTGTTATATATTCAATGCTGAAATTGTAAAAAGAAAGTAGTGTAGA
196 CATTTCACTAGAACTGTTCTTGTTATATATTCAATGCTGAAATTGTAAAAAGAAAGTAGTGTACA
30273449 AAGATTGTAAGTAATCTAGTTACTTTTC
261 AAGATTGTAAGTAATCTAGTTACTTTTC
30273477 CTCTATGTGGCACAAGCATTTCTAGTTGTCGTCTTTCCAAGTTTCTTCATTCTAGATTCTGTTCC
1 CTCTATGTGGCACAAGCATTTCTAGTTGTCGTCTTTCCAAGTTTCTTCATTCTAGATTCTGTTCC
*
30273542 CTTTCTATGGCAACAATAG-ATTGTTCCGATGGCCCATTTTCTTTCTTCTAATGATTGATTTTAT
66 CTTTCTATGGCAACAATAGTATTGGTCCGATGGCCCATTTTCTTTCTTCTAATGATTGATTTTAT
* * *
30273606 ACTCTTCCCTCCATTTGTGAGCATGTGTGTAATTGGGTGATATTTATACATGAGTTTTTGTGCCA
131 ACTCTTCCCTCCATTTGTGAGCATGCGTGTAATTGGGTGATATTTATAAACGAGTTTTTGTGCCA
*
30273671 CATTTCACTAGAACTGTTCTTGTTATATATTCGATGCTGAAATTGTAAAAAGAAAGTAGTGTACA
196 CATTTCACTAGAACTGTTCTTGTTATATATTCAATGCTGAAATTGTAAAAAGAAAGTAGTGTACA
30273736 AAGATTGTAAGTAATCTAGTTACTTTTC
261 AAGATTGTAAGTAATCTAGTTACTTTTC
30273764 CTCT
1 CTCT
30273768 GACCATTATT
Statistics
Matches: 282, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
287 198 0.70
288 84 0.30
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (288 bp):
CTCTATGTGGCACAAGCATTTCTAGTTGTCGTCTTTCCAAGTTTCTTCATTCTAGATTCTGTTCC
CTTTCTATGGCAACAATAGTATTGGTCCGATGGCCCATTTTCTTTCTTCTAATGATTGATTTTAT
ACTCTTCCCTCCATTTGTGAGCATGCGTGTAATTGGGTGATATTTATAAACGAGTTTTTGTGCCA
CATTTCACTAGAACTGTTCTTGTTATATATTCAATGCTGAAATTGTAAAAAGAAAGTAGTGTACA
AAGATTGTAAGTAATCTAGTTACTTTTC
Found at i:30283670 original size:11 final size:11
Alignment explanation
Indices: 30283650--30283694 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
30283640 AGGTCACGTG
*
30283650 GCTGACGTGGT
1 GCTGATGTGGT
30283661 GCTGATGTGGT
1 GCTGATGTGGT
*
30283672 GATGATGTGGT
1 GCTGATGTGGT
30283683 GCTGATGTGGT
1 GCTGATGTGGT
30283694 G
1 G
30283695 ATGCTGACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.11, C:0.09, G:0.47, T:0.33
Consensus pattern (11 bp):
GCTGATGTGGT
Found at i:30283681 original size:22 final size:22
Alignment explanation
Indices: 30283656--30283697 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
30283646 CGTGGCTGAC
30283656 GTGGTGCTGATGTGGTGATGAT
1 GTGGTGCTGATGTGGTGATGAT
30283678 GTGGTGCTGATGTGGTGATG
1 GTGGTGCTGATGTGGTGATG
30283698 CTGACGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.48, T:0.36
Consensus pattern (22 bp):
GTGGTGCTGATGTGGTGATGAT
Found at i:30284223 original size:49 final size:47
Alignment explanation
Indices: 30284169--30284585 Score: 306
Period size: 49 Copynumber: 8.6 Consensus size: 47
30284159 ACAGGGTTCA
*
30284169 CCGTTGCGGCTTAAGCCTTTCCCTTGACATCTTCGTGGTACTGGATTCG
1 CCGTTGCGGCTTAAACCTTTCCCTT--CATCTTCGTGGTACTGGATTCG
* * * * * * *
30284218 TCGTTGCGGCTTAAATCC-TTCCATTTATTTTCTGAGGTACAAGG-TTTG
1 CCGTTGCGGCTTAAA-CCTTTCCCTTCATCTTC-GTGGTAC-TGGATTCG
* **
30284266 CCGTTACGGCTTAAACCTTTCTTTTGACATCTTCGTGGTACTGGATTCG
1 CCGTTGCGGCTTAAACCTTTCCCTT--CATCTTCGTGGTACTGGATTCG
* * * *
30284315 TCGTTGTGGCTTAAATCTTTCCCTTGACATCTTTGTGGTACTGGATTCG
1 CCGTTGCGGCTTAAACCTTTCCCTT--CATCTTCGTGGTACTGGATTCG
* ** * * *
30284364 TCGTTATGGCTTAAATCTTTCCCTTCATACTTCTGAGGTA-TAAGG-TTCT
1 CCGTTGCGGCTTAAACCTTTCCCTTCAT-CTTC-GTGGTACT--GGATTCG
** * *
30284413 CCACTGCGACTTAAACCTTTCCCTCTATATCTTCGTGGTACTGGATTCG
1 CCGTTGCGGCTTAAACCTTTCCCT-T-CATCTTCGTGGTACTGGATTCG
* * *
30284462 CCATTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTA-TAAGG-TTCG
1 CCGTTGCGGCTTAAACCTTTCCCTTCAT-CTTC-GTGGTACT--GGATTCG
* * * *
30284511 CCATTGCGACTTAAACCTTTCCCTTTGTATCTTCGCGGTACTGGATTCG
1 CCGTTGCGGCTTAAACCTTTCCC-TT-CATCTTCGTGGTACTGGATTCG
*
30284560 CCGTTGCGGCTTAAATCTTTCCCTTC
1 CCGTTGCGGCTTAAACCTTTCCCTTC
30284586 GTGGTAATGA
Statistics
Matches: 294, Mismatches: 51, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
47 12 0.04
48 45 0.15
49 209 0.71
50 24 0.08
51 4 0.01
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.39
Consensus pattern (47 bp):
CCGTTGCGGCTTAAACCTTTCCCTTCATCTTCGTGGTACTGGATTCG
Found at i:30284270 original size:97 final size:97
Alignment explanation
Indices: 30284151--30284336 Score: 291
Period size: 97 Copynumber: 1.9 Consensus size: 97
30284141 CTCCTTCATG
* * *
30284151 TCTGAGGTACAGGGTTCACCGTTGCGGCTTAAGCCTTTCCCTTGACATCTTCGTGGTACTGGATT
1 TCTGAGGTACAAGGTTCACCGTTACGGCTTAAACCTTTCCCTTGACATCTTCGTGGTACTGGATT
30284216 CGTCGTTGCGGCTTAAATCCTTCCATTTATTT
66 CGTCGTTGCGGCTTAAATCCTTCCATTTATTT
** **
30284248 TCTGAGGTACAAGGTTTGCCGTTACGGCTTAAACCTTTCTTTTGACATCTTCGTGGTACTGGATT
1 TCTGAGGTACAAGGTTCACCGTTACGGCTTAAACCTTTCCCTTGACATCTTCGTGGTACTGGATT
* *
30284313 CGTCGTTGTGGCTTAAATCTTTCC
66 CGTCGTTGCGGCTTAAATCCTTCC
30284337 CTTGACATCT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 80 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (97 bp):
TCTGAGGTACAAGGTTCACCGTTACGGCTTAAACCTTTCCCTTGACATCTTCGTGGTACTGGATT
CGTCGTTGCGGCTTAAATCCTTCCATTTATTT
Found at i:30284426 original size:98 final size:98
Alignment explanation
Indices: 30284324--30284585 Score: 393
Period size: 98 Copynumber: 2.7 Consensus size: 98
30284314 GTCGTTGTGG
* * * * **
30284324 CTTAAATCTTTCCCTTGACATCTTTGTGGTACTGGATTCGTCGTTATGGCTTAAATCTTTCCCTT
1 CTTAAACCTTTCCCTTGATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
*
30284389 CATACTTCTGAGGTATAAGGTTCTCCACTGCGA
66 CATACTTCTGAGGTATAAGGTTCGCCACTGCGA
*
30284422 CTTAAACCTTTCCCTCT-ATATCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCT
1 CTTAAACCTTTCCCT-TGATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* *
30284486 TCATGCTTCTGAGGTATAAGGTTCGCCATTGCGA
65 TCATACTTCTGAGGTATAAGGTTCGCCACTGCGA
*
30284520 CTTAAACCTTTCCCTTTG-TATCTTCGCGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
1 CTTAAACCTTTCCC-TTGATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
30284584 TC
65 TC
30284586 GTGGTAATGA
Statistics
Matches: 149, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
98 147 0.99
99 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (98 bp):
CTTAAACCTTTCCCTTGATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
CATACTTCTGAGGTATAAGGTTCGCCACTGCGA
Found at i:30284473 original size:147 final size:146
Alignment explanation
Indices: 30284172--30284486 Score: 409
Period size: 147 Copynumber: 2.2 Consensus size: 146
30284162 GGGTTCACCG
** *
30284172 TTGCGGCTTAAGCCTTTCCCTTGACATCTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATCCT
1 TTGCGGCTTAAATCTTTCCCTTGACATCTTCGTGGTACTGGATTCGTCGTTACGGCTTAAATCCT
* * ** * * *
30284237 TCCATTTATTTTCTGAGGTACAAGGTTTGCCGTTACGGCTTAAACCTTTCTTTTGACATCTTCGT
66 TCCATTCATCTTCTGAGGTACAAGGTTTGCCACTACGACTTAAACCTTTCCTCTGACATCTTCGT
* *
30284302 GGTACTGGATTCGTCG
131 GGTACTGGATTCGCCA
* * * *
30284318 TTGTGGCTTAAATCTTTCCCTTGACATCTTTGTGGTACTGGATTCGTCGTTATGGCTTAAATCTT
1 TTGCGGCTTAAATCTTTCCCTTGACATCTTCGTGGTACTGGATTCGTCGTTACGGCTTAAATCCT
* * * *
30284383 TCCCTTCATACTTCTGAGGTATAAGGTTCT-CCACTGCGACTTAAACCTTTCCCTCT-ATATCTT
66 TCCATTCAT-CTTCTGAGGTACAAGGTT-TGCCACTACGACTTAAACCTTT-CCTCTGACATCTT
30284446 CGTGGTACTGGATTCGCCA
128 CGTGGTACTGGATTCGCCA
30284465 TTGCGGCTTAAATCTTTCCCTT
1 TTGCGGCTTAAATCTTTCCCTT
30284487 CATGCTTCTG
Statistics
Matches: 145, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
146 65 0.45
147 76 0.52
148 4 0.03
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (146 bp):
TTGCGGCTTAAATCTTTCCCTTGACATCTTCGTGGTACTGGATTCGTCGTTACGGCTTAAATCCT
TCCATTCATCTTCTGAGGTACAAGGTTTGCCACTACGACTTAAACCTTTCCTCTGACATCTTCGT
GGTACTGGATTCGCCA
Found at i:30297993 original size:14 final size:14
Alignment explanation
Indices: 30297974--30298013 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
30297964 CGTGGCTGAC
30297974 GTGATGCTGATGTG
1 GTGATGCTGATGTG
30297988 GTGA---TGATGTG
1 GTGATGCTGATGTG
*
30297999 GTGATGCTGACGTG
1 GTGATGCTGATGTG
30298013 G
1 G
30298014 CAGTGGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 11 0.50
14 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.45, T:0.33
Consensus pattern (14 bp):
GTGATGCTGATGTG
Found at i:30302221 original size:38 final size:39
Alignment explanation
Indices: 30302179--30302306 Score: 125
Period size: 38 Copynumber: 3.5 Consensus size: 39
30302169 TTTGATTTTG
30302179 AAGGAAAAAGGGA-GAAAATTGAATTTGATTTGAAAAAA
1 AAGGAAAAAGGGATGAAAATTGAATTTGATTTGAAAAAA
* *
30302217 AAGGAAAAATGGATGAAAA--GCCATTTGATTTTG------
1 AAGGAAAAAGGGATGAAAATTG-AATTTGA-TTTGAAAAAA
30302250 AAGGAAAAAGGGA-GAAAATTGAATTTGATTTGAAAAAGA
1 AAGGAAAAAGGGATGAAAATTGAATTTGATTTGAAAAA-A
*
30302289 AA-GAAAAATGGATGAAAA
1 AAGGAAAAAGGGATGAAAA
30302307 GTCATTCCAC
Statistics
Matches: 72, Mismatches: 5, Indels: 25
0.71 0.05 0.25
Matches are distributed among these distances:
32 9 0.12
33 18 0.25
34 1 0.01
37 1 0.01
38 27 0.38
39 16 0.22
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.21
Consensus pattern (39 bp):
AAGGAAAAAGGGATGAAAATTGAATTTGATTTGAAAAAA
Found at i:30302246 original size:71 final size:71
Alignment explanation
Indices: 30302169--30302312 Score: 263
Period size: 71 Copynumber: 2.0 Consensus size: 71
30302159 ATGGTGTTGC
30302169 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTGATTTGAAAAA-AAAGGAAAAATGGATGA
1 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTGATTTGAAAAAGAAA-GAAAAATGGATGA
30302233 AAAGCCA
65 AAAGCCA
30302240 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTGATTTGAAAAAGAAAGAAAAATGGATGAA
1 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTGATTTGAAAAAGAAAGAAAAATGGATGAA
*
30302305 AAGTCA
66 AAGCCA
30302311 TT
1 TT
30302313 CCACCCACGT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 68 0.96
72 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.26
Consensus pattern (71 bp):
TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTGATTTGAAAAAGAAAGAAAAATGGATGAA
AAGCCA
Found at i:30302276 original size:33 final size:33
Alignment explanation
Indices: 30302169--30302280 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
30302159 ATGGTGTTGC
30302169 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAA
1 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAA
* *
30302202 TTTGA-TTTGAAAAAAAAGGAAAAATGGATGAAAA--GCCA
1 TTTGATTTTG------AAGGAAAAAGGGA-GAAAATTG-AA
30302240 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAA
1 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAA
30302273 TTTGATTT
1 TTTGATTT
30302281 GAAAAAGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
32 9 0.14
33 26 0.41
34 1 0.02
37 1 0.02
38 18 0.28
39 9 0.14
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.29
Consensus pattern (33 bp):
TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAA
Found at i:30309056 original size:21 final size:20
Alignment explanation
Indices: 30309032--30309088 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
30309022 TACAATTGTG
30309032 TTAATATTTAATTGTAAATAT
1 TTAATATTTAATT-TAAATAT
30309053 TTAATGA-TTATATTTAAATAT
1 TTAAT-ATTTA-ATTTAAATAT
* *
30309074 TTAAGATATAATTTA
1 TTAATATTTAATTTA
30309089 TATAATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 21 0.68
22 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTAATATTTAATTTAAATAT
Found at i:30309137 original size:24 final size:24
Alignment explanation
Indices: 30309097--30309150 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
30309087 TATATAATCT
* *
30309097 AATTAAAT-TTTATAAATAATTAA
1 AATTAATTATTTAGAAATAATTAA
* *
30309120 TATTAATTATTTAGAAATATTTAA
1 AATTAATTATTTAGAAATAATTAA
30309144 AATTAAT
1 AATTAAT
30309151 ATTCCATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AATTAATTATTTAGAAATAATTAA
Found at i:30312118 original size:54 final size:54
Alignment explanation
Indices: 30312054--30312161 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
30312044 TATTTGAAGT
30312054 GATAAACACTCTGTTTATTAAGTCAATATATAAAATTCTTATCAAAAGTTTTTC
1 GATAAACACTCTGTTTATTAAGTCAATATATAAAATTCTTATCAAAAGTTTTTC
*
30312108 GATAAACACTCTGTTTATTAAGTTAATATATAAAATTCTTATCAAAAGTTTTTC
1 GATAAACACTCTGTTTATTAAGTCAATATATAAAATTCTTATCAAAAGTTTTTC
30312162 ATTCTTAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (54 bp):
GATAAACACTCTGTTTATTAAGTCAATATATAAAATTCTTATCAAAAGTTTTTC
Found at i:30312140 original size:28 final size:28
Alignment explanation
Indices: 30312055--30312141 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
30312045 ATTTGAAGTG
*
30312055 ATAAACACTCTGTTTATTAAGTCAATAT
1 ATAAACACTCTGTTTATTAAGTTAATAT
* * * ** **
30312083 ATAAA-ATTCT-TATCA-AAAGTTTTTCG
1 ATAAACACTCTGT-TTATTAAGTTAATAT
30312109 ATAAACACTCTGTTTATTAAGTTAATAT
1 ATAAACACTCTGTTTATTAAGTTAATAT
30312137 ATAAA
1 ATAAA
30312142 ATTCTTATCA
Statistics
Matches: 40, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
26 11 0.28
27 12 0.30
28 17 0.43
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.40
Consensus pattern (28 bp):
ATAAACACTCTGTTTATTAAGTTAATAT
Found at i:30314384 original size:30 final size:29
Alignment explanation
Indices: 30314316--30314749 Score: 328
Period size: 30 Copynumber: 14.8 Consensus size: 29
30314306 AAGGGGTCAA
*
30314316 AAAATG-AAGTTTCGGAAAATTTAA-GGTT
1 AAAATGTAA-TTTTGGAAAATTTAAGGGTT
* * * *
30314344 AAAATATAATTTTAAGAAAATTTAAGGATC
1 AAAATGTAATTTT-GGAAAATTTAAGGGTT
*
30314374 AAAATGTAATTTTAGGAAAGTTT-AGGGTT
1 AAAATGTAATTTT-GGAAAATTTAAGGGTT
* * *
30314403 AAAATGCAATTTTAGGAAAGTTTAA-GGTC
1 AAAATGTAATTTT-GGAAAATTTAAGGGTT
* *
30314432 AAAATGTAACTTTAGGAAAGTTT-AGGGTT
1 AAAATGTAA-TTTTGGAAAATTTAAGGGTT
* *
30314461 AAAATGTGATTTTAGGAAATTTTAAGGGTT
1 AAAATGTAATTTT-GGAAAATTTAAGGGTT
* * *
30314491 AAAATGTGATGTTGGGAAAGTTT-AGGGTT
1 AAAATGTAAT-TTTGGAAAATTTAAGGGTT
* *
30314520 AATATGTGATTTTGGAAAATTTTAAGGGTT
1 AAAATGTAATTTTGGAAAA-TTTAAGGGTT
* * * *
30314550 AAAATGTGATTTTGGGAAGTTT-AGGGATC
1 AAAATGTAATTTTGGAAAATTTAAGGG-TT
* *
30314579 AAAATGTAATTTTAGAAAAGTTT-GGGGTT
1 AAAATGTAATTTTGGAAAA-TTTAAGGGTT
*
30314608 AAAATGTAATTTTGGAAAAGTTT-AGGGATC
1 AAAATGTAATTTTGGAAAA-TTTAAGGG-TT
* * ** *
30314638 AAAATGTAATTATGGGAAATTTTGGGGATC
1 AAAATGTAATTTTGGAAAATTTAAGGG-TT
* * **
30314668 AAAATGAAATTTTAGAAAAGTTTGGGGGTT
1 AAAATGTAATTTTGGAAAA-TTTAAGGGTT
* * *
30314698 AAAATGTAATTTTAGAAAACTTCAAGGGTA
1 AAAATGTAATTTTGGAAAA-TTTAAGGGTT
*
30314728 AAAATATAATTTTGGAAAATTT
1 AAAATGTAATTTTGGAAAATTT
30314750 TGAGGTTAAA
Statistics
Matches: 336, Mismatches: 54, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
28 23 0.07
29 145 0.43
30 159 0.47
31 9 0.03
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAATTTAAGGGTT
Found at i:30314405 original size:59 final size:58
Alignment explanation
Indices: 30314316--30314771 Score: 404
Period size: 59 Copynumber: 7.7 Consensus size: 58
30314306 AAGGGGTCAA
* * * * * *
30314316 AAAATG-AAGTTTCGGAAAATTTAAGGTTAAAATATAATTTTAAGAAAATTTAAGGATC
1 AAAATGTAA-TTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAATTTAAGGGTC
* *
30314374 AAAATGTAATTTTAGGAAAGTTTAGGGTTAAAATGCAATTTTAGGAAAGTTTAA-GGTC
1 AAAATGTAATTTT-GGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAATTTAAGGGTC
* * * *
30314432 AAAATGTAACTTTAGGAAAGTTTAGGGTTAAAATGTGATTTTAGGAAATTTTAAGGGTT
1 AAAATGTAA-TTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAATTTAAGGGTC
* * * * *
30314491 AAAATGTGATGTTGGGAAAGTTTAGGGTTAATATGTGATTTT-GGAAAATTTTAAGGGTT
1 AAAATGTAAT-TTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAA-TTTAAGGGTC
* * * * *
30314550 AAAATGTGATTTTGGGAAGTTTAGGGATCAAAATGTAATTTTA-GAAAAGTTT-GGGGTT
1 AAAATGTAATTTTGGAAAGTTTAGGG-TTAAAATGTAATTTTAGGAAAA-TTTAAGGGTC
* * * **
30314608 AAAATGTAATTTTGGAAAAGTTTAGGGATCAAAATGTAATTAT-GGGAAATTTTGGGGATC
1 AAAATGTAATTTTGG-AAAGTTTAGGG-TTAAAATGTAATTTTAGGAAAATTTAAGGG-TC
* * * * *
30314668 AAAATGAAATTTTAGAAAAGTTTGGGGGTTAAAATGTAATTTTA-GAAAACTTCAAGGGTA
1 AAAATGTAATTTT-GGAAAGTTT-AGGGTTAAAATGTAATTTTAGGAAAA-TTTAAGGGTC
* * * * *
30314728 AAAATATAATTTTGGAAAATTTTGAGGTTAAAATATGATTTTAG
1 AAAATGTAATTTTGGAAAGTTTAG-GGTTAAAATGTAATTTTAG
30314772 AGAGTTCAAG
Statistics
Matches: 334, Mismatches: 46, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
58 101 0.30
59 175 0.52
60 49 0.15
61 9 0.03
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGGAAAATTTAAGGGTC
Found at i:30316644 original size:48 final size:48
Alignment explanation
Indices: 30316572--30316693 Score: 199
Period size: 48 Copynumber: 2.5 Consensus size: 48
30316562 TTCTTGGTAT
* ** *
30316572 ACTTCTCTGTATCTCATCAGGAAGATGACCGTTTTATTACTTTGACCC
1 ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCC
30316620 ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCC
1 ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCC
*
30316668 ACTTCTCTGTATCTCATCAAAAAGAT
1 ACTTCTCTGTATCTCATCAAGAAGAT
30316694 AAAGGTTTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35
Consensus pattern (48 bp):
ACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCC
Found at i:30317053 original size:206 final size:209
Alignment explanation
Indices: 30316619--30317188 Score: 673
Period size: 207 Copynumber: 2.7 Consensus size: 209
30316609 TACTTTGACC
* * * * * * ** * *
30316619 CACTTCTCTGTATCTCATCAAGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGTATCTCA
1 CACTTCTCTGCATCTCGTTAGGAAGATAACCACTTTATTGCTTTAAACCACTTCTATGTATCTCA
** ** * ** * ** * * ** * *
30316684 TCAAAAAGATAAAGGTTTGAAGCCTCATTCGTATTGAGTTTTACTTCATCGATTTGGTCTACTTT
66 TCAGGAAGATAGGGGTTTAAAGTTTCACTCACATTAAGCTTCGCTTCATTGATTTGGTCTACTTC
30316749 TCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGA
131 TCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGA
30316814 AGACGGATTTGGTT
196 AGACGGATTTGGTT
* * *
30316828 CACTTCTCTGCATCTCGTTAGGAAGATGACCTCTTTATTGCTTT-GA-CACTTCTATGTATCTCA
1 CACTTCTCTGCATCTCGTTAGGAAGATAACCACTTTATTGCTTTAAACCACTTCTATGTATCTCA
* *
30316891 TCAGGAAGAT-GGGGTTTAAAAGTTTCACTCACATTGAGCTTCGCTTCATTGAATTGGTCTACTT
66 TCAGGAAGATAGGGGTTT-AAAGTTTCACTCACATTAAGCTTCGCTTCATTGATTTGGTCTACTT
* * * *
30316955 CTCTGTATCTCATCAGGAAGATGACTGTTTCGTTG-TTTAATCCT-CTTCTTTGTATCTCATCAG
130 CTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAAT-CTACTTCTCTGTATCTCATCAG
*
30317018 GAAGATGGATTTGGTT
194 GAAGACGGATTTGGTT
* *
30317034 CACTTCTGTGCATCTCGTTAGGAAGATAACCACTTTATTGCTTTAAACCACTTCTCTGTATCTCA
1 CACTTCTCTGCATCTCGTTAGGAAGATAACCACTTTATTGCTTTAAACCACTTCTATGTATCTCA
* * * * * * *
30317099 TTAGGAAGATAGGGGTTTGAGGTTTCATTCACATTAAGCTTTGCTTCATTGTTTTGGTCTGCTTC
66 TCAGGAAGATAGGGGTTTAAAGTTTCACTCACATTAAGCTTCGCTTCATTGATTTGGTCTACTTC
*
30317164 TCTGTATCTCATCAAGAAGATGACC
131 TCTGTATCTCATCAGGAAGATGACC
30317189 TTTTGAAGTT
Statistics
Matches: 309, Mismatches: 47, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
206 85 0.28
207 93 0.30
208 87 0.28
209 44 0.14
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (209 bp):
CACTTCTCTGCATCTCGTTAGGAAGATAACCACTTTATTGCTTTAAACCACTTCTATGTATCTCA
TCAGGAAGATAGGGGTTTAAAGTTTCACTCACATTAAGCTTCGCTTCATTGATTTGGTCTACTTC
TCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCTACTTCTCTGTATCTCATCAGGA
AGACGGATTTGGTT
Found at i:30317247 original size:38 final size:38
Alignment explanation
Indices: 30317198--30317321 Score: 122
Period size: 38 Copynumber: 3.2 Consensus size: 38
30317188 CTTTTGAAGT
*
30317198 TTCACTCTTCCCTATGATCAGGGTAAGATATCGTATGC
1 TTCAATCTTCCCTATGATCAGGGTAAGATATCGTATGC
* * * * *
30317236 TTCAATTTTCCCTATGATCGGGGTCAGGTACTGGTATGTC
1 TTCAATCTTCCCTATGATCAGGGTAAGATA-TCGTATG-C
* * * * * *
30317276 TTCAATCTGCCCTTTGATCAGGATAAAAGATCGGATGC
1 TTCAATCTTCCCTATGATCAGGGTAAGATATCGTATGC
30317314 TTCAATCT
1 TTCAATCT
30317322 ACGCCGTGGT
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
38 34 0.51
39 11 0.16
40 22 0.33
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (38 bp):
TTCAATCTTCCCTATGATCAGGGTAAGATATCGTATGC
Found at i:30318226 original size:41 final size:42
Alignment explanation
Indices: 30318176--30318255 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
30318166 TTTGGTTTCA
* *
30318176 AGACACCCTTTGCGGGTTTTCATCTCAAT-CTTTTTTTATCG
1 AGACACCCTTTACGGATTTTCATCTCAATCCTTTTTTTATCG
* *
30318217 AGACGCCCTTTACGGATTTTCATGTCAATCCTTTTTTTA
1 AGACACCCTTTACGGATTTTCATCTCAATCCTTTTTTTA
30318256 GGCGAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.44
Consensus pattern (42 bp):
AGACACCCTTTACGGATTTTCATCTCAATCCTTTTTTTATCG
Found at i:30324488 original size:24 final size:24
Alignment explanation
Indices: 30324461--30324515 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
30324451 ATCTTTCATA
30324461 TCCTTATAC-ATTCTTGTCATTTGT
1 TCCTTATACTATTCTTG-CATTTGT
*
30324485 TCCTGTA-ACTGTTCTTGCATTTGT
1 TCCT-TATACTATTCTTGCATTTGT
30324509 T-CTTATA
1 TCCTTATA
30324516 TCTCTCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
23 3 0.11
24 14 0.52
25 8 0.30
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (24 bp):
TCCTTATACTATTCTTGCATTTGT
Found at i:30328400 original size:29 final size:28
Alignment explanation
Indices: 30328368--30328788 Score: 299
Period size: 29 Copynumber: 14.3 Consensus size: 28
30328358 AGTTTCAGAG
*
30328368 AATTTAGGGTTAAAATATAATTTTAGGAA
1 AATTTAGGGTTAAAATGTAATTTT-GGAA
*
30328397 AATTTAGGGATAAAAAAT-TAATTTTAGGAA
1 AATTTAGGG-T-TAAAATGTAATTTT-GGAA
* * *
30328427 AGTTTAAGGGTTGAAATG-AGATTTTATGAA
1 AATTT-AGGGTTAAAATGTA-ATTTT-GGAA
* *
30328457 AATTTAGGGTTAAAATGTGATTTCTAGAA
1 AATTTAGGGTTAAAATGTAATTT-TGGAA
** * * * *
30328486 GGTTTGGGGTCAAAATATAATTTTGAAA
1 AATTTAGGGTTAAAATGTAATTTTGGAA
* * *
30328514 AACTTAAGGGTTAAAATATTATTTTAGGAA
1 AA-TTTAGGGTTAAAATGTAATTTT-GGAA
* *
30328544 AATTTAGGGTTAAAATGTGATTTTGGGA
1 AATTTAGGGTTAAAATGTAATTTTGGAA
*
30328572 AGTTTAGGGGTTAAAATGT-ATTTTGGAA
1 AATTTA-GGGTTAAAATGTAATTTTGGAA
*
30328600 AAGTTTAGGGGTTAAAATGTAGTTTTGTGAA
1 AA-TTTA-GGGTTAAAATGTAATTTTG-GAA
* * * * **
30328631 AGTTAAAGGATCAAAATACAATTTTGGAA
1 AATT-TAGGGTTAAAATGTAATTTTGGAA
* * *
30328660 AAGTTTGAGTGGTCAAAATGCAATTTGGGAA
1 AA-TTT-AG-GGTTAAAATGTAATTTTGGAA
*
30328691 AGTTTAGGGATTAAAATGTAATTTTGGAA
1 AATTTAGGG-TTAAAATGTAATTTTGGAA
* * *
30328720 AAGTTTGGCGGTTAAAATCTAATTTTGAAA
1 AA-TTTAG-GGTTAAAATGTAATTTTGGAA
* *
30328750 AAGTTTAGAGGTTAAAATGTAACTTTGAAA
1 AA-TTTAG-GGTTAAAATGTAATTTTGGAA
30328780 AATTTAGGG
1 AATTTAGGG
30328789 GGTCAAAATA
Statistics
Matches: 316, Mismatches: 56, Indels: 41
0.77 0.14 0.10
Matches are distributed among these distances:
28 24 0.08
29 143 0.45
30 114 0.36
31 35 0.11
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (28 bp):
AATTTAGGGTTAAAATGTAATTTTGGAA
Found at i:30328437 original size:60 final size:58
Alignment explanation
Indices: 30328370--30328788 Score: 300
Period size: 60 Copynumber: 7.1 Consensus size: 58
30328360 TTTCAGAGAA
*
30328370 TTTAGGGTTAAAATATAATTTTAGGAAAATTTAGGGATAAAAAAT-TAATTTTAGG-AAAG
1 TTTAGGGTTAAAATATAATTTT-GGAAAATTTAGGGAT-TAAAATGTAATTTT-GGAAAAG
* * * * * *
30328429 TTTAAGGGTTGAAATGA-GATTTTATGAAAATTTAGGG-TTAAAATGTGATTTCTAG-AAGG
1 TTT-AGGGTTAAAAT-ATAATTTT-GGAAAATTTAGGGATTAAAATGTAATTT-TGGAAAAG
* * * * * *
30328488 TTTGGGGTCAAAATATAATTTTGAAAAACTTAAGGG-TTAAAATATTATTTTAGGAAAA-
1 TTTAGGGTTAAAATATAATTTTGGAAAA-TTTAGGGATTAAAATGTAATTTT-GGAAAAG
* * * * *
30328546 TTTAGGGTTAAAATGTGATTTTGGGAAGTTTAGGGGTTAAAATGT-ATTTTGGAAAAG
1 TTTAGGGTTAAAATATAATTTTGGAAAATTTAGGGATTAAAATGTAATTTTGGAAAAG
* * * * * * **
30328603 TTTAGGGGTTAAAATGTAGTTTTGTGAAAGTTAAAGGATCAAAATACAATTTTGGAAAAG
1 TTTA-GGGTTAAAATATAATTTTG-GAAAATTTAGGGATTAAAATGTAATTTTGGAAAAG
* ** * *
30328663 TTTGAGTGGTCAAAATGCAATTTGGGAAAGTTTAGGGATTAAAATGTAATTTTGGAAAAG
1 TTT-AG-GGTTAAAATATAATTTTGGAAAATTTAGGGATTAAAATGTAATTTTGGAAAAG
* * * * *
30328723 TTTGGCGGTTAAAATCTAATTTTGAAAAAGTTTAGAGG-TTAAAATGTAACTTT-GAAAAA
1 TTTAG-GGTTAAAATATAATTTTGGAAAA-TTTAG-GGATTAAAATGTAATTTTGGAAAAG
30328782 TTTAGGG
1 TTTAGGG
30328789 GGTCAAAATA
Statistics
Matches: 287, Mismatches: 56, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
56 6 0.02
57 21 0.07
58 85 0.30
59 60 0.21
60 97 0.34
61 18 0.06
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
TTTAGGGTTAAAATATAATTTTGGAAAATTTAGGGATTAAAATGTAATTTTGGAAAAG
Found at i:30331006 original size:18 final size:18
Alignment explanation
Indices: 30330983--30331018 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
30330973 ATTATTAGAA
30330983 ATAAATTAT-TTTTTATTT
1 ATAAA-TATGTTTTTATTT
30331001 ATAAATATGTTTTTATTT
1 ATAAATATGTTTTTATTT
30331019 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATAAATATGTTTTTATTT
Found at i:30334800 original size:6 final size:6
Alignment explanation
Indices: 30334789--30334822 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30334779 AGCCGACCAT
* *
30334789 GAAGAG GAAGAG GAAGAG GAAGTG GAGGAG GAAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAG
30334823 CGTGACGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.03
Consensus pattern (6 bp):
GAAGAG
Found at i:30344857 original size:19 final size:20
Alignment explanation
Indices: 30344828--30344913 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
30344818 AAAATTGTTC
30344828 AAATATTATAGTAAATTTAG
1 AAATATTATAGTAAATTTAG
* *
30344848 AAAT-TTATAGGAAATCTTTG
1 AAATATTATAGTAAAT-TTAG
*
30344868 AAA-ATTAT-TTAAAATTTA-
1 AAATATTATAGT-AAATTTAG
*
30344886 AAATACTATAG-AAATTTAG
1 AAATATTATAGTAAATTTAG
*
30344905 AAAAATTAT
1 AAATATTAT
30344914 TATATATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
18 10 0.20
19 23 0.45
20 18 0.35
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.38
Consensus pattern (20 bp):
AAATATTATAGTAAATTTAG
Found at i:30346667 original size:77 final size:77
Alignment explanation
Indices: 30346573--30346748 Score: 205
Period size: 77 Copynumber: 2.3 Consensus size: 77
30346563 CTCCTAGAAT
* * * *
30346573 TAAAA-TTCATCACCTTTTTATCTTCTTAT-TCTAACTTGAAATTATATATTATACC-TCTTTAA
1 TAAAATTTCAT-ATCTTTTTATCTTCTTATCT-TAACTTAAAATCATATATTAT-CCTTCTTCAA
*
30346635 AAATTCAAGCAAAAA
63 AAATTCAAACAAAAA
* *
30346650 TAAAATTTCATATCTTTTTATCTTCTTATCTTAATTTAAAATCATATATTGTCCTTCTTCAAAAA
1 TAAAATTTCATATCTTTTTATCTTCTTATCTTAACTTAAAATCATATATTATCCTTCTTCAAAAA
* *
30346715 TTCAAATAGAAA
66 TTCAAACAAAAA
* *
30346727 TAGAATTCCATATCTTTTTATC
1 TAAAATTTCATATCTTTTTATC
30346749 CTAACTAGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
76 2 0.02
77 77 0.91
78 6 0.07
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (77 bp):
TAAAATTTCATATCTTTTTATCTTCTTATCTTAACTTAAAATCATATATTATCCTTCTTCAAAAA
TTCAAACAAAAA
Found at i:30346814 original size:33 final size:33
Alignment explanation
Indices: 30346730--30346814 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
30346720 ATAGAAATAG
**
30346730 AATTCCATATCTTTTTATCCTAACTAGAATTCA
1 AATTCCATATCTTTAAATCCTAACTAGAATTCA
**
30346763 AATGGC-T-TCTTTTCAAATCCTAA-TAGAATTCA
1 AATTCCATATC-TTT-AAATCCTAACTAGAATTCA
30346795 AATTCCATATCTTTGAAATC
1 AATTCCATATCTTT-AAATC
30346815 ATTTACTCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
31 2 0.05
32 17 0.41
33 20 0.49
34 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (33 bp):
AATTCCATATCTTTAAATCCTAACTAGAATTCA
Found at i:30348791 original size:22 final size:22
Alignment explanation
Indices: 30348738--30348792 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
30348728 ATAAATACAT
30348738 ATATAGGGTTCGTATGATAAAC
1 ATATAGGGTTCGTATGATAAAC
* *
30348760 ATACAGGGTTTGTAT-ATACAAC
1 ATATAGGGTTCGTATGATA-AAC
*
30348782 ATATAAGGTTC
1 ATATAGGGTTC
30348793 TCCATAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (22 bp):
ATATAGGGTTCGTATGATAAAC
Found at i:30349023 original size:27 final size:27
Alignment explanation
Indices: 30348959--30349029 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
30348949 ATGGGGATTC
* *
30348959 GTCTATAGGGATTCGCGTATTGGGTTA
1 GTCTATAGGGGTTCACGTATTGGGTTA
* *
30348986 GCCTATAGGGGTTCACGTATTGGGTTT
1 GTCTATAGGGGTTCACGTATTGGGTTA
30349013 GTCTATAGGGGCTTCAC
1 GTCTATAGGGG-TTCAC
30349030 ATATAGGGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 33 0.87
28 5 0.13
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.35
Consensus pattern (27 bp):
GTCTATAGGGGTTCACGTATTGGGTTA
Found at i:30353733 original size:21 final size:20
Alignment explanation
Indices: 30353702--30353743 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
30353692 AAGAGTTTTA
30353702 AAATGTAAATTTACAAAAAAAT
1 AAATGTAAA-TTA-AAAAAAAT
30353724 AAAT-TAAATTAAAAAAAAT
1 AAATGTAAATTAAAAAAAAT
30353743 A
1 A
30353744 TTAAACTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 4 0.20
22 4 0.20
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATGTAAATTAAAAAAAAT
Found at i:30354832 original size:26 final size:26
Alignment explanation
Indices: 30354796--30354858 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
30354786 TCAAGTTTAT
*
30354796 GTACCAAAGTGAATAAAAAAATATAA
1 GTACCAAAGTGAATAAAAAAATACAA
*
30354822 GTACCAAAGTGAATGAAAAAATACAA
1 GTACCAAAGTGAATAAAAAAATACAA
30354848 GTACCAAAGTG
1 GTACCAAAGTG
30354859 GGGACCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.17
Consensus pattern (26 bp):
GTACCAAAGTGAATAAAAAAATACAA
Found at i:30355074 original size:23 final size:24
Alignment explanation
Indices: 30355038--30355082 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
30355028 TAGTCATTTA
*
30355038 TTTTAAATTTTTTATT-TAAAAGC
1 TTTTAAATTATTTATTATAAAAGC
*
30355061 TTTTAAGTTATTTATTATAAAA
1 TTTTAAATTATTTATTATAAAA
30355083 ATAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTAAATTATTTATTATAAAAGC
Found at i:30360749 original size:20 final size:19
Alignment explanation
Indices: 30360711--30360749 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
30360701 TAACATCATT
*
30360711 AATTAATCTTGTTTAATTA
1 AATTAATCTGGTTTAATTA
*
30360730 AATTAATCATGGTTTTATTA
1 AATTAATC-TGGTTTAATTA
30360750 TCATAATCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (19 bp):
AATTAATCTGGTTTAATTA
Found at i:30376003 original size:18 final size:19
Alignment explanation
Indices: 30375982--30376018 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30375972 ATATTTTATC
*
30375982 CATAGAAAA-TATTAAAAA
1 CATAAAAAATTATTAAAAA
30376000 CATAAAAAATTATTAAAAA
1 CATAAAAAATTATTAAAAA
30376019 TTGATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (19 bp):
CATAAAAAATTATTAAAAA
Found at i:30376054 original size:10 final size:9
Alignment explanation
Indices: 30376004--30376083 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 9
30375994 TAAAAACATA
30376004 AAAAATTATT
1 AAAAATTA-T
30376014 AAAAATTGAT
1 AAAAATT-AT
*
30376024 ATAAACTTAT
1 A-AAAATTAT
*
30376034 AAATATTAT
1 AAAAATTAT
30376043 AAAAAGTTAT
1 AAAAA-TTAT
* *
30376053 -AAATTTTT
1 AAAAATTAT
*
30376061 AATAAATTCT
1 AA-AAATTAT
*
30376071 AATAATTAT
1 AAAAATTAT
30376080 AAAA
1 AAAA
30376084 TAAAATAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
8 3 0.06
9 22 0.41
10 23 0.43
11 6 0.11
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (9 bp):
AAAAATTAT
Found at i:30376054 original size:19 final size:20
Alignment explanation
Indices: 30376001--30376056 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
30375991 TATTAAAAAC
*
30376001 ATAAAAAATTATTAAAAATTG
1 ATAAAAAATTA-TAAATATTG
* *
30376022 ATATAAACTTATAAATATT-
1 ATAAAAAATTATAAATATTG
*
30376041 ATAAAAAGTTATAAAT
1 ATAAAAAATTATAAAT
30376057 TTTTAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
20 7 0.23
21 9 0.30
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (20 bp):
ATAAAAAATTATAAATATTG
Found at i:30377396 original size:13 final size:13
Alignment explanation
Indices: 30377374--30377403 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30377364 GTTGCCACGT
30377374 CACCAGCTGCCAC
1 CACCAGCTGCCAC
*
30377387 CACCATCTGCCAC
1 CACCAGCTGCCAC
30377400 CACC
1 CACC
30377404 GTCACCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.57, G:0.10, T:0.10
Consensus pattern (13 bp):
CACCAGCTGCCAC
Found at i:30379130 original size:29 final size:29
Alignment explanation
Indices: 30379078--30379331 Score: 194
Period size: 29 Copynumber: 8.7 Consensus size: 29
30379068 TTTGACTCCC
* * *
30379078 AAACTTCTCAAAAATTATAATTTTACCCAT
1 AAACTTC-CAAAAATCACATTTTTACCCAT
*
30379108 AAACTTCCAAAAACCACATTTTTA-CCAT
1 AAACTTCCAAAAATCACATTTTTACCCAT
* * * * * *
30379136 CGAGCTTCTTAAAAATTACATTTTTGCCCTT
1 -AAACTTC-CAAAAATCACATTTTTACCCAT
* *
30379167 AAACTTCCAAAAATCACATTTTGACCC-C
1 AAACTTCCAAAAATCACATTTTTACCCAT
* *
30379195 AAACTTCTCAAAAATTACATTTTTGTCCCA-
1 AAACTTC-CAAAAATCACATTTTT-ACCCAT
* **
30379225 AAACTTCCAAAAATCACGTTTTTACCCCC
1 AAACTTCCAAAAATCACATTTTTACCCAT
* *
30379254 AAACTTCCAAAAATAACA-TTTTACCCTT
1 AAACTTCCAAAAATCACATTTTTACCCAT
* * * *
30379282 GAACTTCTCAAAAATTATATTTTTTATCCCCT
1 AAACTTC-CAAAAATCACA-TTTTTA-CCCAT
30379314 -AACTTCCAAAAATCACAT
1 AAACTTCCAAAAATCACAT
30379332 CCAAAAATCA
Statistics
Matches: 178, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
28 28 0.16
29 88 0.49
30 44 0.25
31 14 0.08
32 4 0.02
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCACATTTTTACCCAT
Found at i:30379211 original size:58 final size:58
Alignment explanation
Indices: 30379044--30379331 Score: 269
Period size: 59 Copynumber: 4.9 Consensus size: 58
30379034 CCCAGAAGGT
* * * * * *
30379044 CCTTGAACTGTCCAGAAATCATATTTTGACTCCCAAACTTCTCAAAAATTATAATTTTAC
1 CCTTAAACT-TCCAAAAATCACATTTTTAC-CCCAAACTTCTCAAAAATTACATTTTTAC
* * * * * * *
30379104 CCATAAACTTCCAAAAACCACATTTTTACCATCGAGCTTCTTAAAAATTACATTTTTGC
1 CCTTAAACTTCCAAAAATCACATTTTTACC-CCAAACTTCTCAAAAATTACATTTTTAC
* *
30379163 CCTTAAACTTCCAAAAATCACATTTTGACCCCAAACTTCTCAAAAATTACATTTTTGTC
1 CCTTAAACTTCCAAAAATCACATTTTTACCCCAAACTTCTCAAAAATTACATTTTT-AC
* * *
30379222 CC-AAAACTTCCAAAAATCACGTTTTTACCCCCAAACTTC-CAAAAATAACA-TTTTAC
1 CCTTAAACTTCCAAAAATCACATTTTTA-CCCCAAACTTCTCAAAAATTACATTTTTAC
* * * * *
30379278 CCTTGAACTTCTCAAAAATTATATTTTTTATCCCCTAACTTC-CAAAAATCACAT
1 CCTTAAACTTC-CAAAAATCACA-TTTTTA-CCCCAAACTTCTCAAAAATTACAT
30379332 CCAAAAATCA
Statistics
Matches: 187, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
56 3 0.02
57 10 0.05
58 63 0.34
59 104 0.56
60 7 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
CCTTAAACTTCCAAAAATCACATTTTTACCCCAAACTTCTCAAAAATTACATTTTTAC
Done.